Best Accounting Apps for Shopify in 2025

Streamline your ecommerce business with Webgility's Modern Commerce Workspace, meticulously crafted for seamless integration with QuickBooks and popular platforms like Shopify, Amazon, WooCommerce, Etsy, and more. Say goodbye to time-consuming accounting tasks and manual inventory updates. Webgility automates the recording of online orders, customers, sales tax, and fees directly into your accounting solution, eradicating the need for data entry, CSV files, and spreadsheets.

Key Benefits:

• Effortless Bookkeeping: Bid farewell to manual bookkeeping. Webgility automates the process, ensuring your financials are always up to date.
• Seamless Financial Closure: Closing your books becomes a hassle-free task, allowing you to focus on strategic aspects of your business.
• Simplified Sales Tax Filing: Webgility simplifies sales tax filing, saving you time and ensuring compliance with tax regulations.
• Effortless Compliance: Compliance with regulations is effortless with Webgility, allowing you to navigate complex requirements effortlessly.
• Collaborative Accounting: Collaborate seamlessly with your accountant, ensuring smooth communication and effective financial management.

Refrens is the best invoice generator as you can create unlimited invoices for unlimited clients without paying a single amount. 

With just one click, you may generate a delivery challan, payment receipt, debit note, and credit note.

The invoice's fields and columns can also be changed at any time, and you have full freedom to transmit the document by email or WhatsApp or save it as a PDF and send it immediately.

Even if you use an online invoice generator, making invoices might be really difficult if you're one of the business owners who prepares bills at the end of the month. It takes time to create an invoice, send it to your client, and repeat the procedure, especially if you have a lot of invoices that need to be paid by the end of the month.

But after the sheet is published, the system will generate invoices using the bulk invoices you input using Refrens' invoice generator. You can create GST invoices, Non-GST invoices, and GST e-invoices using the bulk invoices tool.

You can focus on expanding your business while saving a tonne of time and work by using a free online invoice creator like Refrens.

Key Features: 

• Free Unlimited Invoice
• Permission control
• Quick Easy Invoice
• Customization of Columns
• Email & Track Invoices
• Recurring Invoices
• Custom Formula 
• Invoice Templates
• Insightful Reports
• Client Management
• Ready Data
• Free invoice generator 
• International Payment gateaway
• User friendly

Effortless Shopify accounting made possible with A2X. Trusted by thousands of stores, this one-click solution simplifies the reconciliation process. A2X automatically posts summarized journals to your Xero, QuickBooks, or Sage ledger using the invoice API, transforming Shopify transactions into easily manageable 'invoices'.

Key Benefits:

• Tailored for Shopify: Built specifically for Shopify store accountants and bookkeepers, A2X streamlines your accounting processes.
• Perfect Reconciliation: A2X ensures flawless reconciliation, eliminating discrepancies and ensuring your financial records are accurate.
• Efficient Tidying: Say goodbye to messy books. A2X tidies up your accounts, making your financial data organized and comprehensible.
• Shopify Plus & Shopify POS Integration: Seamlessly integrate with Shopify Plus and Shopify POS systems, ensuring comprehensive coverage for all your Shopify transactions.
• Multi-Platform Support: A2X isn't limited to Shopify. It works seamlessly across various ecommerce platforms, providing multi-channel support for the most popular platforms worldwide.
• Customizable Mapping: Use A2X's standard Shopify chart of accounts or customize your mapping to align Shopify and payment gateway transactions with your chart of accounts. A2X monitors your Shopify Store, automatically detecting payouts, and posting sales and fees to your accounting ledger, saving you valuable time.

Automate, Customize, Summarize and Analyze any Data (2000 data fields) in your Store! Data Export Reposrts app provides fine level detail and summary of the data.

Each Shopify store is unique and its reporting needs are different. Data Export team of reporting experts will create the right custom report or dashboard. Our team has created more than 10,000 custom reports for Shopify merchants. We also believe a reporting app should not cost more than the Shopify plan itself.

Key Features:

• Sales Reports
• Tax reports
• Cost of sales report
• POS Reports
• Shopify Payout reports.
• Custom fields
• Customer Reports
• Fulfillment Reports
• Shopify Reports
• Discount Reports
• Refund Reports
• Product Reports
• Other Reports

Streamlined accounting in no time!

Integrate your shopify store and the german lexoffice accounting software with a few easy steps and get your accounting process streamlined.

You can use any fields from the order to enhance you invoices pre- and posttexts to make them more personal.

Have your invoices ready for your tax attorney in the popular DATEV format which is supported by lexoffice.

Please note: As this app is targeting the german speaking market only, the App UI is in german.

Recommended browsers: Microsoft Edge, Google Chrome, Firefox, Safari

Missed out on keeping your accounting straight? No worries, unlock the historical import feature to get any order from your store into your lexoffice account.

Key Features:

• Booking of OSS-relevant documents (tax reform 2021)
• More security and faster loading times through Session Token
• Precisely define delivery date / service date & delivery period / service period
• Reporting of sales per customer in lexoffice
• Transfer of company name from Shopify checkout to lexoffice
• Mark Invoices due when creating them. Save another click and precious time!
• Small Business Owner? We got you covered. Create Invoices without taxes.
• Create Lexoffice invoices for your Shopify orders automatically
• Send customers their invoices via email automatically
• Booking of OSS-relevant documents (tax reform 2021)
• Sync POS orders with Lexoffice
• Exclude sales tax if you are a "Kleinunternehmer"
• Update invoices automatically for refunds or partial refunds
• Import past Shopify orders
• Individual invoice layouts – including layout designer