How do you find the right accounting app for your Shopify store? There's a wide selection of tools available – but which solution is truly a good fit for your business model, your processes, and your tax advisor? Especially in e-commerce, it's crucial that invoices are created automatically, accurately, and in compliance with GoBD (German Accounting Standards) – ideally including payment reconciliation and DATEV export. Choosing the wrong setup here will result in duplicate work or trouble with your annual financial statements.
In this article, we compare the most popular accounting software for Shopify and show you which solutions have proven themselves in practice – from simple invoicing apps to fully automated accounting systems. You'll learn which app is suitable for whom, what to look for when choosing, and which pitfalls to avoid.
This overview is based on our experience working with numerous Shopify merchants and close collaboration with the team at Pathway Solutions – our top recommendation for automated, legally compliant e-commerce accounting .
1. Why should you use accounting apps on Shopify?
E-commerce accounting is anything but trivial – especially if you sell on Shopify. Although Shopify offers a powerful e-commerce platform, it lacks an integrated accounting solution tailored to the German market. This leaves many retailers facing a multitude of challenges: manual invoicing, complicated VAT regulations for international sales, and different payment providers with their own fee structures – all of this can quickly lead to errors that prove costly later on.
In addition, Germany has strict accounting requirements, from GoBD compliance to legally compliant invoice archiving and the transfer of all data to the tax advisor in DATEV format. Without the right tools, this usually means a lot of manual effort, Excel chaos, and uncertainty.
Accounting apps close precisely this gap. They help you record Shopify orders in a legally compliant manner, create invoices automatically, and handle your accounting digitally, efficiently, and error-free – so you can focus on what really matters: your business.
Learn more about the most common challenges and biggest hurdles in our guide to accounting on Shopify .
2. What functions does good accounting software perform?
2.1. Automated, legally compliant invoice creation
Manual invoicing is time-consuming and error-prone. Good accounting apps automatically create invoices for every order – GoBD-compliant, tamper-proof, and archived for audit-proof purposes. Particularly important: Invoices must not be subsequently amendable to comply with legal requirements.
2.2. DATEV export for tax consultants
One of the most important features is the seamless DATEV export, so all accounting-relevant data flows directly into your accountant's system. Tools like Pathway Accounting Export Pro automatically convert Shopify transactions into a DATEV-compatible format—including payments, fees, returns, credit notes, and more.
You can find out more about connecting Shopify to DATEV in our guide.
2.3. Automated payment reconciliation with payment providers
Good accounting software not only takes into account Shopify data, but also payment flows via PayPal, Klarna, Shopify Payments , and others. This is the only way to correctly record income and fees – a point at which many basic solutions like Lexoffice quickly reach their limits without additional tools.
2.4. VAT logic & OSS support
Especially for international sales, correct calculation and accounting of VAT according to country-specific tax rates is crucial. Pathway, for example, supports both OSS reporting and reverse charge procedures for B2B customers in the EU.
2.5. Multilingual and customizable invoices
Tools such as Pathway or Sofiu offer the possibility of creating multilingual invoices with individual logos or mandatory text for each country – essential for international retailers with a strong brand focus.
2.6. Digital Archiving & GDPR Compliance
All receipts and accounting data must be stored in an audit-proof manner and protected from unauthorized access. Accounting apps handle complete archiving so that no documents are lost—ideal for tax audits or annual financial statements.
2.7. Scalability & Workflow Integration
As your shop grows, your accounting software should also keep pace. While Order Printer is sufficient for small shops, ERP systems like Plentymarkets or specialized tools like Pathway are a better choice for increasing order volumes. Important: The software should be flexible and integrate well into your existing setup.
3. The most popular accounting software in comparison
Since Shopify, as a Canadian provider, doesn't offer an accounting solution specifically tailored to the German market, merchants rely on external apps to manage their accounting efficiently and in compliance with legal requirements. Depending on your needs—whether simple invoicing, payment reconciliation, or complete accounting automation—there are various tools that have proven successful in the Shopify community. We've taken a closer look at the most popular solutions:
3.1. Our recommendation: Pathway Solutions – The complete solution for Shopify accounting
- Suitable for: Merchants looking for fully automated, DATEV-compatible accounting software.
- Invoice Printer Pro: Automatic, GoBD-compliant invoice creation with DATEV export.
- Accounting Export Pro : Automated reconciliation between Shopify, payment providers and DATEV.
- Special feature: Specially optimized for German accounting requirements.
Assessment: Pathway Solutions is one of the few tools that generates legally compliant invoices and offers seamless DATEV integration.
3.2. Order Printer & Order Printer Pro – The basic solution for invoices
- Suitable for: Small shops that need simple invoicing within Shopify.
- Order Printer: Basic tool (free) enables the printing of invoices and packing slips.
- Order Printer Pro: Advanced features such as automated invoice creation and customized templates.
Assessment: A cost-effective solution for merchants with minimal accounting overhead. However, it's not ideal for legally compliant accounting, as it requires manual work and doesn't offer automation with tax advisors.
3.3. Lexoffice – Accounting software with Shopify interface
- Suitable for: Merchants looking for all-in-one accounting software with invoicing and tax features.
- Features: Creation and management of invoices, direct interface to Shopify, VAT calculation & DATEV export for tax advisors.
Assessment: Well-known accounting software, but not specifically optimized for Shopify – the processes are often not as automated as with Shopify-specific solutions.
3.4. Sufio – High-quality invoicing with a design focus
- Suitable for: Merchants who value professionally designed invoices.
- Features: Automatic invoice creation for each order, design templates, support for credit notes & refunds.
Assessment: Perfect for merchants who want brand-compliant invoices. However, it's more expensive than other solutions and not the best choice for tax automation.
3.5. Bilbee – ERP-Light with accounting functions
- Suitable for: Retailers who want to combine inventory management & invoicing.
- Functions: Multichannel accounting, invoicing, DATEV export, focus on warehouse & inventory management.
Assessment: Flexible, especially for retailers with multiple sales channels. However, it is often too complex and expensive for purely accounting purposes.
3.6. Pickware, WeClapp & Plentymarkets – ERP systems with accounting modules
- Suitable for: Scaling retailers who need a complete ERP system with integrated accounting.
- Features: Comprehensive inventory management & automation, integrated invoicing & accounting, export options for DATEV.
Assessment: ERP systems are worthwhile for large shops with numerous orders and complex logistics. However, they are often oversized for small and medium-sized Shopify stores.
Not just accounting: Every merchant should know these top Shopify apps .
4. Pathway as an invoicing solution
Correct invoicing is essential for Shopify merchants to both comply with legal requirements and ensure efficient accounting. Pathway offers Invoice Printer Pro, a solution that integrates seamlessly with Shopify and creates all invoices automatically, in a legally compliant, and tamper-proof manner. The direct connection to DATEV digitizes the entire invoicing process and simplifies data exchange with tax advisors.
Many retailers still rely on manual invoicing or use basic solutions. However, these allow subsequent changes to invoices, which is not GoBD-compliant in Germany. Pathway's Invoice Printer Pro, on the other hand, ensures that all invoices are immutable and tamper-proof.
4.1. Advantages of Invoice Printer Pro > DATEV
- 100% compliant with German market requirements → GoBD & GDPR compliant invoicing.
- Tamper-proof invoice documentation → Invoices once created can no longer be changed.
- Automatic invoice creation → Every order immediately receives a legally compliant invoice, which is sent directly to the customer.
- DATEV export → Invoice data is transferred seamlessly into the tax advisor’s DATEV system.
- Digital archiving → All invoices are stored in an audit-proof manner and comply with legal retention requirements.
Multilingual invoices are also becoming increasingly important for Shopify merchants who sell internationally. Pathway supports:
- Automatic creation of invoices in multiple languages → Perfect for international sales.
- Different logos per country → For a professional brand presence in every market.
- Tax-compliant VAT mapping → Including OSS support for EU-wide trade.
- Correct calculation of VAT on shipping costs → adaptation to the applicable tax rates of each country.
B2B sales are also optimally supported:
- Reverse charge procedure for B2B invoices → Correct tax processing for business customers in the EU.
- Individual invoice contents for local regulations → Example: Recycling fees as a separate item for France.
- e-Invoice → All invoices can optionally be created via ZUGFERD format.
5. Automatic accounting export with Pathway and DATEV
As order volume increases, so does the complexity of accounting – for example, in payment reconciliation, sales tax, or collaboration with the tax office. Pathway supports this precisely: The solution automates central accounting processes, ensures structured data capture, and facilitates transfer to DATEV. This saves time, reduces errors, and creates a solid foundation for professional financial management in e-commerce.
Detailed information on Pathway's accounting and export functions can be found in our article on connecting Shopify and DATEV .
