Shopify ERP: Why merchants benefit from a good inventory management system and which ERP Shopify integrations make e-commerce easier

E-commerce businesses are complex: sales channels, inventory movements, and customer expectations are all growing at the same time. According to bevh, the German online retail sector generated 83.1 billion euros in merchandise sales in 2025, up from 80.6 billion the previous year. Anyone looking to grow in this environment needs streamlined processes and readily available data. A Shopify ERP delivers exactly that. In this article, you’ll learn how Shopify ERP integration works, which ERP programs are suitable for your online store, and what you should look for when making your selection.

Shopify ERP at a Glance

What’s it about? This article explains how merchants can connect an ERP system or inventory management solution with Shopify and Shopify Plus, and which system suits which needs.

Who is it for? Shopify merchants and e-commerce managers in the DACH region.

Key points:

1. An ERP system connects the store, warehouse, purchasing, accounting, and shipping through a shared database. Orders, inventory, and prices are automatically synchronized.

2. There are three integration methods: a certified ERP app from the Shopify App Store, an ERP connector or middleware, or a custom API integration.

3. Certified local ERP apps are offered by Xentral, Pickware, JTL, plentymarkets, Actindo, and Afterbuy, among others. Microsoft Dynamics 365 and SAP are typically integrated through an implementation partner.

4. An ERP system is worthwhile for businesses with high order volumes, multiple channels or warehouses, overselling, production or product bundles, and growing administrative burdens.

5. Key factors to consider when selecting a system include e-commerce focus, Shopify integration, scalability, automation, e-invoicing, total cost of ownership, and operating model (cloud or on-premises).

6. E-invoicing has been mandatory for receiving invoices in B2B since 2025. For sending invoices, it will be phased in starting in 2027 (for companies with prior-year revenue exceeding 800,000 euros) and 2028 (for all companies).

What is an ERP system?

ERP stands for Enterprise Resource Planning. An ERP system is a suite of software solutions that helps a company implement resource planning and manage business processes. ERP software typically has a modular structure, allowing companies to combine individual software modules according to their specific needs.

ERP integration, on the other hand, means connecting an ERP (enterprise resource planning) system with other software applications, databases, or systems used within a company.

The main goal of this integration is to ensure a seamless flow of information and smooth collaboration between different departments and business processes.

Why is ERP integration important?

A modern company typically uses many different software solutions for different functions, such as:

• Customer relationship management (CRM) for sales and marketing

• E-commerce platforms for online sales

• Warehouse management systems (WMS) for logistics and inventory management

• Manufacturing execution systems (MES) for production control

• Financial software for accounting and general ledger management

Simply put, ERP integration means that your ERP system works seamlessly with other tools.

Common examples:

• E-commerce ↔ ERP Orders from the online store are sent directly to the ERP, and inventory levels in the ERP update the store in real time.

• CRM ↔ ERP Customer data and quotes from the CRM flow into the ERP, while invoices from the ERP are synchronized back with the CRM.

• Accounting ↔ ERP Transactions and payments are automatically exchanged between the ERP and the accounting software.

• Logistics/Shipping ↔ ERP Shipping status and tracking numbers are synchronized directly into the ERP.

Types of ERP Systems: On-Premises vs. Cloud-Based ERP Systems

ERP integrations are no longer just for large corporations. More and more ERP providers are targeting small and medium-sized enterprises (SMEs) with their solutions. Over time, two primary models for ERP programs have emerged:

1. On-premises software

On-premises software runs on a server. In this model, ERP software is licensed for local installation. Companies therefore need their own hardware, such as computers and servers.

On-premise ERP systems are usually suitable for large companies and corporations. Due to the complexity of these companies, the set-up takes a long time and costs are high, but the requirements can be well mapped.

2. Cloud ERP systems

Cloud ERP is a software-as-a-service (SaaS) solution that allows users to access the ERP software package online via a web browser. An installation on a company computer does not have to be done. ERP cloud providers usually use a rental model, which means that you as a retailer get all the components you need for a monthly flat rate and do not have to worry about maintenance, repairs and updates.

This variant is particularly suitable for SMEs, as the set-up is much faster and there is no need to set up an IT department. These solutions are also scalable and grow with the company’s requirements.

Benefits of a Shopify ERP System in E-Commerce

The use of enterprise resource planning systems is now firmly established in e-commerce, regardless of the size of a company. ERP systems facilitate numerous work steps and organization. Some systems have a wide range of functions and also include warehouse logistics, for example.

In short, the use of ERP systems is cost-saving, time-saving and minimizes the workload. The following advantages stand out in particular:

1. With an ERP integration, you can establish efficient warehousing, reduce inventory, shorten lead times and increase delivery capacity.

2. With an ERP system, you can make production planning and control more efficient using bills of materials and centralized data management.

3. By linking Shopify and ERP, you create an effective controlling system that optimizes your financial flows and budget planning. Due to the uniform data basis, you will no longer lose any data and reporting will be simplified.

4. With an ERP system, comprehensive information is available to you in bundled form, enabling you to manage staff optimally and make strategic decisions.

5. ERP systems unify processes - you no longer need several individual tools, everything is combined.

6. In addition to the general clarity, information silos disappear thanks to central document management and existing documents are archived appropriately.

7. Only a central database enables intensive relationships with customers without losing the overview, analyzing past processes and submitting precisely fitting offers.

In summary, with an ERP system you will be able to provide more transparency, efficiency, better communication and optimized customer care.

Functions of ERP Systems: The Most Important ERP Application Modules

Modern ERP systems cover all areas and business processes of a company. With ERP software, all business divisions have access to a common database, so that functional boundaries are abolished. ERP programs include various basic modules as well as add-on modules that can be added as required.

Materials management and logistics

Materials management includes planning, managing, and controlling material flows within the company and between the company and stakeholders such as customers and suppliers. The term material covers everything from raw materials to finished products. An ERP system allows you to keep track of all material movements – from procurement to storage to dispatching. The combination of Shopify and ERP allows fulfillment automation, which can be a valuable competitive advantage in fast-paced online business.

Production

Production is the core function of many industrial companies and is a key component of ERP software. Production planning and control (PPS for short) is a comprehensive component and requires interfaces with many other business areas.

For example, it must be clear exactly what materials are needed for production and in what quantities. As a result, the production department is closely integrated with procurement and sales. With systems like Xentral, bills of materials and production orders can be linked directly to Shopify orders (Xentral Production).

Finance and accounting

The recording and monitoring of cash and benefits flows by finance and accounting are simplified by an ERP system. While internal accounting focuses on controlling and cost management, external accounting is responsible for clean accounting and reporting to the outside world.

Solutions are available for both internal and external processes that automate tasks such as payments, reminders or depreciation, etc. For companies with multiple subsidiaries or cost centers, the controlling module is essential. Providers such as Microsoft Dynamics 365 and SAP have an advantage in this area.

Human Resources

Human Resources is responsible for personnel management and all related tasks. This module brings together personnel planning, recruitment and development as well as operational tasks such as payroll accounting.

Time recording systems can also be used to record all working, personnel and machine hours.

Customer Relationship Management (CRM)

Extensive opportunities in the areas of marketing and sales are bundled in a CRM module. Today, products and services are often sold through multiple channels. You therefore particularly benefit from linking Shopify with ERP. Centralized data management is essential to build an intensive customer relationship.

This creates the opportunity to offer first-class customer service and carry out coordinated marketing activities.

Master data management

Central master data management is the heart of an ERP system. This ensures smooth operations based on consistent data records. Not only different systems for the same data, but also additional information from individual departments or employees can inhibit the flow of information in the company.

Advantages: Centralized data management greatly improves data quality throughout the company. Inconsistencies and redundancies are eliminated, and there is no longer a need for duplicate entries or manual data updates, resulting in time and cost savings.

Document management

Similar to the management of (customer) data, various workflows and documents are created in individual departments. Paper documents such as invoices and digital documents such as e-mails are captured by document management and centrally organized.

The database can be searched according to any criteria, allowing all areas of the company to access documents and workflows. With the link Shopify and ERP, you no longer get lost in the paper economy.

Interfaces

Due to the complexity of enterprises, the number of data sources is increasing. A modern ERP system offers further interfaces to e-commerce solutions, for example, to ensure a holistic view of the company.

As an e-commerce company, these interfaces are extremely important to ensure a smooth process across all important channels and not to lose track.

Shopify ERP Integration: The Shopify ERP Program for Europe

Alongside its global ERP program, which includes Microsoft Business Central and Oracle NetSuite, Shopify offers a local ERP program for Europe. It launched in October 2022. Local ERP providers develop their own Shopify-certified apps for the program. The first partners in Germany included Actindo, Afterbuy, JTL, Pickware, plentymarkets, and Xentral.

With this program, local ERP providers offer merchants a direct solution through the Shopify App Store. This means you no longer need to develop your own interface for standard processes such as order import, inventory reconciliation, and product data. An API connection remains an option for custom processes.

When is ERP integration for Shopify really worthwhile?

ERP integration with Shopify becomes essential when your business growth exceeds the capacity of manual processes.

It is necessary if you are facing one or more of the following critical challenges:

Key triggers for integration

• High volume & errors: You have a high number of daily orders, which leads to significant time spent on manual data entry (from Shopify to accounting/processing) and frequent human errors.

• Inventory issues: You sell through multiple channels (Shopify, Amazon, retail) or use multiple warehouses, and the lack of real-time inventory synchronization constantly leads to overselling and customer dissatisfaction.

• Complex operations: Your business involves processes that go beyond simple sales, such as manufacturing, kitting, or complex procurement, which require the robust management tools of an ERP system.

• Scaling bottleneck: Administrative tasks (reporting, reconciliation, inventory management) consume too much of your team's time and prevent the business from scaling efficiently without hiring additional administrative staff.

• New legal requirements: You must receive or, in the future, issue e-invoices (XRechnung/ZUGFeRD), and your invoicing system is not yet set up for this.

Latori Expert Tip: Avoid data silos and manual intermediate steps.

As your online store scales, manually transferring data between Shopify and external systems often leads to delays and errors. An automated connection between Shopify and your ERP keeps inventory and order data synchronized across all channels in real time.

How to Set Up a Shopify ERP Integration—Step by Step

Phase 1: Analysis and design (what and why)

• Understand and document processes: Record the current workflow from ordering to accounting. Identify specifically: Where do bottlenecks occur? Where do manual errors happen?

• Define data sovereignty and synchronization goals: Precisely define which data needs to be synchronized – typically orders, inventory levels, and prices. Determine which system is the leading system (system of record) for which type of data. Usually, the ERP system takes on this role.

• Select a technical solution: Choose a connection method: (1) an ERP app from the Shopify App Store, (2) an ERP connector or middleware (iPaaS), or (3) a custom integration via the Shopify Admin API (GraphQL).

Phase 2: Implementation and testing (the how)

• Create data mapping: Create a detailed mapping table that documents exactly which field in Shopify corresponds to which field in the ERP.

• Set up a test environment: Set up a completely isolated test environment, such as a Shopify Development Store. Never test directly on the live system!

• Perform comprehensive test scenarios: Simulate all business cases: standard orders, cancellations, returns, discounts, and special cases. Pay particular attention to checking the real-time synchronization of inventory levels.

Latori Expert Tip: Eliminate Sources of Error Before Go-Live

Assign a unique SKU to each variant that is identical in both systems. Discrepancies in SKUs are one of the most common causes of incorrect inventory levels. Also, test partial returns, bundles, discount codes, and international orders with different tax rates, and set up notifications for failed synchronizations after launch.

Phase 3: Productive launch and monitoring (go-live)

• Clean up master data: Ensure that all master data for products, customers, and categories is consistent and up to date in both systems.

• Activate the system: Activate the integration in live operation.

• Monitoring and training: Closely monitor the interface for errors or anomalies during the first few weeks. Train your team in parallel with the new automated workflows and processes.

How to Choose the Right ERP System (Including E-Invoicing)

Industry-specific requirements

An ERP system should be precisely tailored to the specific requirements of the e-commerce sector, as the industry relies heavily on the smooth and efficient handling of business processes. In addition to inventory management, which ensures that there are always enough goods in stock, shipping logistics and returns management must also be optimally integrated. Especially in e-commerce companies, where orders need to be processed quickly and returns handled efficiently, automated and seamless process control is crucial in order to save time and resources. Another key feature of an industry-specific ERP system is support for multichannel sales. As many e-commerce retailers are active on different platforms such as Shopify, Amazon or eBay, the ERP system should be able to centrally manage and synchronise orders and data from these channels.

Scalability

Retailers should take care to choose an ERP system that not only meets their current needs, but is also flexible and scalable in the long term. A growing company will have to cope with greater challenges over time, such as a greatly expanded product range, an increasing number of orders or the connection of additional sales channels. The ERP system should be able to cope with these increased requirements without causing performance bottlenecks.

Integration with existing systems

An ERP system must not only be seamlessly integrated with the platforms and tools already in use, such as the Shopify shop, CRM software or accounting programmes, but also have flexible interfaces to enable future extensions or changes. Simple and smooth integration saves companies valuable time during implementation and prevents common errors that can occur during manual data synchronisation. In addition, deep integration ensures that real-time data flows between systems, improving decision-making processes and increasing efficiency.

User-friendliness

An ERP system should not only be easy to understand and intuitive to use, but also offer a customisable user interface that meets the specific needs of different departments. A high level of user-friendliness minimises the amount of training required and ensures that employees can familiarise themselves with the system more quickly, which significantly increases efficiency in day-to-day operations. A user-friendly structure also minimises the risk of operator errors, resulting in more accurate data entry and smoother processes.

Costs

When choosing an ERP system, the total costs over the entire life cycle should be taken into account. This includes not only the initial cost of the system, but also the cost of implementation, staff training and ongoing maintenance. It is crucial that these costs are clearly defined and transparently itemised to enable realistic budget planning. Companies should also take into account hidden costs such as possible customisations, support contracts or updates. This is the only way to ensure that the ERP system fits into the company budget in the long term and that no unexpected financial burdens arise.

E-Invoicing and Compliance

The ERP system should be able to generate and process e-invoices. The requirement to receive e-invoices in B2B transactions has been in effect since January 1, 2025, and mandates structured formats in accordance with EN 16931, such as XRechnung and ZUGFeRD. A phased implementation applies to sending e-invoices: Starting January 1, 2027, companies with prior-year revenue exceeding 800,000 euros must issue e-invoices; starting January 1, 2028, the requirement applies to all domestic B2B companies. A plain PDF does not count as an e-invoice, as it does not contain structured data. Small businesses as defined in Section 19 of the German Value-Added Tax Act (UStG) are exempt from this requirement. You should also verify GoBD-compliant archiving and integration with your accounting system.

Latori Expert Tip: Ask e-invoicing providers specific questions

Ask every ERP provider specifically: “Does your system generate and receive XRechnung and ZUGFeRD without an additional module, and how is this triggered from a Shopify order?” The answer will quickly reveal how mature the solution is.

Cloud-based vs. on-premise

When choosing an ERP system, companies need to carefully consider whether they want to opt for a cloud-based solution or an on-premise version. Cloud-based ERP systems offer a high degree of flexibility and enable access to the system from anywhere, which is particularly advantageous for decentralised teams or international companies. In addition, the upfront costs are usually lower, as no expensive hardware infrastructure is required on site, and regular updates and maintenance are taken care of by the provider.

On the other hand, on-premise solutions offer more control, as the data is stored locally on the company's servers, which can be a major advantage in sensitive industries with strict data protection guidelines.

Automations

An ERP system should be able to fully automate essential business processes such as inventory management, invoicing or the creation of reports in order to significantly reduce manual effort. This not only saves time and resources, but also minimises the susceptibility to errors in recurring tasks. This allows organisations to focus more on strategic activities, increase operational efficiency and make decisions based on accurate, automatically generated data. In addition, automation leads to a faster response to changes in the market or in order volumes.

Our recommendation: 6 Top ERP systems for Shopify

As a Shopify merchant, you have many ERP programs to choose from. The right ERP system for your Shopify store depends on its size, processes, and budget. We’ll show you 6 ERP systems with Shopify integration that we have experience with.

Pickware

Pickware is a partner in the Shopify ERP program. Pickware ERP merchandise management is a comprehensive solution that has been specially developed for online retailers who want to manage their processes efficiently and centrally. It combines warehouse, shipping, invoices, returns, purchasing and accounting in one system. Products, orders and stock from Shopify, marketplaces and retail stores can be easily managed, while barcode scanners and extensively integrated shipping service providers ensure automated processes.

For Shopify in particular, Pickware offers a high-performance cloud solution that enables orders to be imported in real time. The user-friendly interface is intuitively designed and ideally tailored to the needs of online retailers. This means that no complex familiarization with the system is necessary. The offer is complemented by personal support, which impresses with fast response times and individual solutions.

For our mutual client Bodyshake, we integrated Pickware with the Shopify Plus store. Read the linked Bodyshake case study for more details.

Xentral

The Xentral ERP Business Software bundles all business areas in one place and automates workflows. With the lean ERP system, you can keep track of everything from logistics to all e-commerce activities to accounting. The cloud-based Xentral ERP covers all important functions.

Via API interfaces, many third-party tools can be integrated into Xentral’s ERP software with just a few clicks. In this way, individual processes can be automated step by step. The Cloud ERP from Xentral is available in different price packages in the subscription.

Working closely with COEUR DE LION, we have established Shopify Plus and Xentral’s ERP in the company to enable the company to continue to grow. The Xentral ERP system can now also be integrated directly via an app in the Shopify App Store. This was programmed by Latori in collaboration with Xentral.

Download Xentral App now

Microsoft Dynamics D365

With the expandable ERP, operations can be automated across departments. The ERP system offers a wealth of functions and the ability to integrate external data. The user interface is designed intuitively in line with other Microsoft products. Individual applications can be used independently, combined with each other or integrated into external tools. The Microsoft Dynamics offering is available as a software solution in the cloud or on-premise. In the past, we have already been able to support some customers with the integration of the MS Dynamics ERP system. Outdoorchef, the leading Swiss manufacturer of gas kettle grills, relied on Latori's services to integrate Microsoft Dynamics D365, a powerful ERP system, with Shopify. Mister Spex also relies on the know-how of Latori for the migration of its Norwegian contact lens shop Lensit to Shopify Plus and for the connection to the ERP system MS Dynamics.

SAP

Probably the best known player on the market of ERP systems is SAP. For example, while Xentral’s ERP software is aimed at SMEs, SAP is also and above all suitable for large companies. SAP offers can be requested as an on-premise, i.e. local installation, as well as in the Software-as-a-Service model.

With this ERP all business areas can be automated. Due to the range of functions and the complex installation, both advice and onboarding from the expert are recommended. By the way, the Latori team can also help you here!

plentymarkets

The plentymarkets e-commerce ERP system simplifies the day-to-day work of e-commerce companies with numerous modules and linking all important channels.

The cloud-based ERP software provides comprehensive features and interfaces to automate the entire multichannel distribution for retailers. plentymarkets also offers its ERP subscription in different packages.

Shape Republic is one of the leading retailers in the area of feelgood food for women. Together with Latori, the company migrated from Magento to Shopify Plus. In addition to the general time pressure and customer-specific solutions for the online shop, we have integrated the cloud-based ERP system plentymarkets, the fulfilment solution odc and the Emarsys Customer Engagement Platform to create a seamless multi-channel solution.

JD Edwards

JD Edwards' ERP software suite provides a powerful, fully integrated system that supports on-premises, cloud, and hybrid deployments. More than 80 application modules offer great flexibility for the automation of important business areas.

The wide range of functions and wide-ranging industry solutions make this ERP system particularly interesting for large companies.

Sennheiser, one of the best-known manufacturers of headphones and soundbars, uses Shopify Plus and the JD Edwards ERP system. The company relied on Latori for the technical implementation. JD Edwards was integrated with Shopify via EDIFACT.

The six ERP systems at a glance

Conclusion

ERP systems offer you a comprehensive overview of your company. As an online retailer, you benefit from the connection between Shopify and ERP systems, above all by simplifying work and saving time. With ERP software, you have all important data centrally available and easily keep track of multiple sales channels, goods movements and customers.

A Shopify ERP is especially worthwhile if manual data transfers are time-consuming, if you’re dealing with multiple channels or warehouses, or if e-invoicing is changing your processes. Start with your processes, not the tool, and test all edge cases before going live.