Best Shopify Integrations for Accounting & Automation

If you are running a Shopify store with more than a handful of orders per day, you already know the pain of manual bookkeeping. Every order generates revenue, shipping charges, discounts, tax collected, payment gateway fees, and (frequently) refunds. Multiply that by 50, 200, or 1,000 orders per day and the data entry becomes a full-time job -- one that adds zero strategic value to your business.

Manual processes break in predictable ways:

• Accuracy collapses at scale. One miskeyed digit in a spreadsheet cascades into incorrect VAT filings, wrong profit margins, and stock discrepancies that take hours to trace.
• Reconciliation becomes a nightmare. Shopify batches dozens of orders into a single bank payout. Without an integration that breaks the payout down into its components (gross sales, fees, refunds, net deposit), matching your bank feed to your books is guesswork.
• Inventory drift. If your accounting system does not reflect real-time stock levels and COGS, you are making purchasing and pricing decisions based on stale data.
• Time cost. Merchants report spending 5--15 hours per week on manual bookkeeping tasks that an integration eliminates entirely.

Shopify integrations fall into three broad categories, and most growing stores need at least one from each:

1. Accounting integrations -- sync sales, fees, refunds, and tax to your accounting platform (QuickBooks, Xero, Sage)
2. Inventory integrations -- track stock levels, COGS, and manufacturing across warehouses and sales channels
3. Payment integrations -- reconcile multi-gateway payouts (Stripe, PayPal, Shopify Payments) with your general ledger

This guide covers the best tools in each category, with honest pricing, feature comparisons, and recommendations based on your store's size and complexity. No affiliate links, no sponsorships -- just an independent breakdown of Shopify integrations that actually work.

Accounting integrations are the foundation of any Shopify automation stack. They ensure that every sale, refund, fee, and payout is recorded in your accounting software accurately and on time. The right tool depends on which accounting platform you use, how many orders you process, and whether you sell across multiple channels or currencies.

Here are the six best Shopify accounting integrations available in 2026, ranked by capability and value.

The Shopify Connector by Intuit is QuickBooks Online's native integration for Shopify. It is free, officially supported by Intuit, and available directly from the Shopify App Store.

What it does: The connector syncs Shopify orders, refunds, and payouts to QuickBooks Online. It creates invoices or sales receipts in QBO for each Shopify order and maps revenue, discounts, shipping, and tax to the corresponding QBO accounts. Payouts are matched to your bank feed for reconciliation.

Pricing: Free (included with any QuickBooks Online subscription).

Strengths:

• Zero cost -- no monthly fee beyond your existing QBO subscription
• Official Intuit product, so it is updated alongside QBO itself
• Straightforward setup with a guided mapping wizard
• Decent for single-channel, single-currency stores with moderate volume

Limitations:

• No multi-currency support -- a significant gap for European sellers
• No COGS or inventory tracking
• No support for Amazon, eBay, or other channels -- Shopify only
• Limited control over how data is summarised (per-order only, not per-payout)
• User reviews cite occasional sync delays and mapping inflexibility

Best for: Solo Shopify merchants using QuickBooks Online with a single currency and fewer than 100 orders per month who want a free, no-fuss connection.

A2X is the gold standard for e-commerce accounting integrations, trusted by thousands of accountants and bookkeepers worldwide. It creates per-payout summaries that break down every Shopify deposit into its components: gross sales, fees, refunds, discounts, shipping, and tax.

Pricing: EUR 19--99/month depending on order volume. Plans scale from Mini (200 orders/month) to Beyond (10,000+ orders/month).

Accounting platforms supported: QuickBooks Online, Xero, Sage.

Strengths:

• Per-payout reconciliation that matches your bank feed exactly -- the easiest method for clean books
• COGS tracking on higher-tier plans
• Multi-channel support: Shopify, Amazon, eBay, Etsy, Walmart, BigCommerce
• Rated 4.8/5 across app stores -- consistently the highest-rated e-commerce accounting app
• Audit-ready output that accountants trust

Limitations:

• Multi-currency support is limited compared to some competitors
• Higher-volume plans become expensive (EUR 99/month for 10,000+ orders)
• Setup requires careful account mapping -- not a one-click install

Best for: Growing to high-volume Shopify stores that want clean, per-payout accounting in QBO, Xero, or Sage. The go-to choice for merchants who work with an accountant or bookkeeper.

Synder is a multi-platform accounting sync tool that connects over 20 payment and e-commerce platforms to your accounting software. It handles Shopify alongside Stripe, PayPal, Square, Amazon, Etsy, and more -- making it the most versatile option for merchants with complex payment stacks.

Pricing: EUR 20--200/month. The Medium plan (EUR 55/month) covers 1,000 transactions; the Scale plan (EUR 200/month) covers 50,000 transactions.

Accounting platforms supported: QuickBooks Online, QuickBooks Desktop, Xero, Sage.

Strengths:

• Connects 20+ platforms in a single dashboard -- ideal for merchants selling on Shopify, Amazon, and Etsy simultaneously
• Per-transaction or summary sync modes -- you choose the granularity
• Full multi-currency support with automatic exchange rate handling
• Smart Rules engine for automated categorisation of unusual transactions
• Inventory tracking on higher-tier plans

Limitations:

• The pricing scales steeply at high volumes -- EUR 200/month for the Scale plan
• The interface can feel overwhelming with 20+ connected platforms
• Some users report slower sync speeds compared to A2X

Best for: Multi-channel, multi-gateway merchants who need a single tool to consolidate Shopify, Amazon, Stripe, PayPal, and more into one accounting feed. Particularly strong for EU sellers dealing with multiple currencies.

Webgility is a full accounting automation platform purpose-built for e-commerce. It goes beyond simple data sync -- Webgility automates the entire accounting workflow from order to reconciliation, including automated posting, tax mapping, and inventory updates.

Pricing: EUR 49--249/month. The Pro plan (EUR 99/month) covers most mid-sized stores; the Premium plan (EUR 249/month) adds advanced automation and priority support.

Accounting platforms supported: QuickBooks Online only (no Xero or Sage support).

Strengths:

• The deepest QuickBooks integration available -- automates posting, reconciliation, and reporting end-to-end
• Full inventory sync between Shopify and QuickBooks, including COGS and stock adjustments
• Multi-channel: Shopify, Amazon, eBay, Walmart, Etsy, WooCommerce
• Automated tax code mapping that handles US sales tax complexity well
• Dedicated onboarding support with guided setup

Limitations:

• QuickBooks Online only -- no Xero or Sage support, which limits its appeal for European merchants
• The most expensive option in this comparison at EUR 249/month for Premium
• Steeper learning curve due to the depth of automation features

Best for: High-volume QuickBooks Online users who want full end-to-end accounting automation, not just data sync. If your accounting platform is QBO and you want maximum automation, Webgility is the most powerful option available.

Amaka offers a simple, affordable Shopify-to-accounting sync that is ideal for small stores that need basic automation without complexity. It syncs daily sales summaries to your accounting platform with minimal configuration.

Pricing: Free (up to 100 orders/month) or EUR 25/month for unlimited orders.

Accounting platforms supported: QuickBooks Online, Xero, MYOB.

Strengths:

• The most affordable option -- genuinely free for small stores
• Clean, simple interface with a setup process that takes under 10 minutes
• COGS tracking included on the paid plan
• Supports both QBO and Xero, making it versatile for European merchants

Limitations:

• No multi-currency support
• No multi-channel support -- Shopify, Square, or single-channel only
• Daily summary sync only -- no per-payout or per-order granularity
• Limited reporting and customisation compared to A2X or Synder

Best for: Solo merchants and small stores processing fewer than 100 orders per month who want a free or very low-cost way to get Shopify data into Xero or QuickBooks without manual entry.

FinTask takes a different approach to Shopify accounting integration. Rather than simply syncing transaction data, FinTask applies AI-powered automation to the entire accounting workflow -- from data capture and categorisation to reconciliation, anomaly detection, and reporting.

Pricing: Custom plans based on transaction volume. Free trial available.

Accounting platforms supported: Xero, QuickBooks Online.

Strengths:

• Multi-channel by design: connect Shopify alongside Amazon, WooCommerce, Stripe, PayPal, and more in a single unified workflow
• AI-powered categorisation: transactions are automatically categorised based on historical patterns, with confidence scores so you know when to review
• Intelligent reconciliation: FinTask matches payouts to clearing account entries and flags mismatches before you open your accounting software
• Anomaly detection: unexpected fee spikes, duplicate entries, and unusual refund patterns are flagged in real time
• European-first: built for multi-currency, multi-country VAT, and EU regulatory requirements from the ground up
• Works alongside existing integrations (A2X, Synder, etc.) as an automation layer

Limitations:

• Not a direct Shopify-to-accounting data pipe -- FinTask is an automation layer that works on top of your integration stack
• Custom pricing means you need to contact the team for a quote

Best for: European merchants running multi-channel operations who want AI accounting tools with seamless Shopify integration -- not just data sync, but genuine automation of the accounting tasks that still require human judgement. Particularly strong for businesses already using Xero or QuickBooks that want to eliminate manual reconciliation and review.

Accounting integrations handle the financial side, but if you sell physical products, you also need to track stock levels, COGS, and supply chain operations. Shopify's built-in inventory tracking is adequate for simple stores, but it falls short for businesses with manufacturing, multi-warehouse operations, or high SKU counts. Here are the best Shopify inventory integrations for 2026.

Katana is a cloud manufacturing and inventory management platform designed for makers and product-based businesses. It connects to Shopify for order management and to Xero or QuickBooks for accounting -- giving you a complete production-to-sale-to-books pipeline.

Pricing: From EUR 129/month (Starter plan). The Standard plan (EUR 349/month) adds advanced manufacturing features.

Key features:

• Manufacturing focus: bill of materials (BOM), production scheduling, raw material tracking, and shop floor management
• Real-time inventory: live stock levels across Shopify, Amazon, WooCommerce, and your physical warehouse
• COGS and landed cost tracking: accurate cost calculations including shipping, customs, and overhead
• Shopify integration: auto-sync orders, allocate stock, and update availability in real time
• Integrates with Xero and QuickBooks Online for accounting

Best for: Product-based businesses that manufacture or assemble goods and need to track raw materials, production costs, and finished goods inventory alongside their Shopify sales. If you have a BOM, Katana is purpose-built for your workflow.

Cin7 (formerly DEAR Systems) is a comprehensive inventory management platform built for multi-channel e-commerce. It connects Shopify, Amazon, WooCommerce, eBay, and B2B sales channels to a single inventory hub, with native integrations to Xero and QuickBooks for accounting.

Pricing: From EUR 349/month (Cin7 Core Standard plan). Cin7 Omni pricing is on request.

Key features:

• Multi-channel inventory: centralised stock management across every sales channel with automatic quantity sync
• Warehouse management: pick, pack, and ship workflows with barcode scanning and 3PL integrations
• COGS journal entries: automated cost of goods sold sync to Xero via journal entries
• Invoice consolidation: group high-volume e-commerce invoices by day or month before syncing to Xero
• Manufacturing: production planning, BOM, and assembly tracking

Best for: Mid-sized to large e-commerce businesses selling across multiple channels that need enterprise-grade inventory management with deep Xero integration. See our full guide to Cin7 Shopify integration for a detailed setup walkthrough.

Trunk is a lightweight inventory sync tool that keeps stock levels consistent across Shopify, Amazon, eBay, Etsy, Walmart, and other channels. It does not try to be a full inventory management platform -- it focuses on doing one thing well: preventing overselling by syncing quantities in real time.

Pricing: From approximately EUR 35/month for the Merchant plan.

Key features:

• Real-time quantity sync: stock level changes on one channel are reflected across all connected channels within minutes
• Bundling and kitting: create product bundles that automatically deduct component inventory when sold
• Safety stock: set buffer quantities per channel to avoid overselling during sync delays
• Simple setup: connect your channels and map your SKUs -- no complex configuration required

Best for: Multi-channel sellers who need reliable inventory sync without the complexity or cost of a full inventory management platform. If your main problem is overselling because stock levels are out of sync between Shopify and Amazon, Trunk solves it simply and affordably. See our guide to Shopify inventory sync for more options.

Payment integrations bridge the gap between your payment gateways and your accounting software. Shopify Payments (powered by Stripe) is the default, but many merchants also accept PayPal, manual bank transfers, and other gateways. Each gateway has its own fee structure, payout schedule, and reporting format -- which is why payment reconciliation is one of the most time-consuming tasks in e-commerce accounting.

Stripe Reconciliation

If you use Shopify Payments, you are already using Stripe under the hood. Stripe handles card processing, fee deduction, and payout batching. The challenge is reconciling Stripe payouts in your accounting software -- each deposit contains multiple orders with fees deducted, and the amounts rarely match individual Shopify orders.

Tools like A2X, Synder, and FinTask excel at Stripe reconciliation. They break down each payout into its components (gross sales, Stripe fees, refunds, net deposit) and post a matching entry to your accounting software. This means your bank deposit matches a single entry in your books, making reconciliation a one-click process.

PayPal Integration

PayPal adds another layer of complexity because it holds funds in a separate PayPal balance before transferring to your bank account. This creates a timing difference: Shopify records the sale immediately, but the cash may not reach your bank for days. You need a dedicated PayPal clearing account in your accounting software and an integration that tracks PayPal deposits separately from Shopify Payments deposits.

Synder handles PayPal particularly well, syncing PayPal transactions alongside Shopify and Stripe in a unified dashboard. A2X also supports PayPal reconciliation on its higher-tier plans.

Multi-Gateway Management

Merchants accepting payments through Shopify Payments, PayPal, Klarna, Apple Pay, and manual transfers need a separate clearing account for each gateway in their accounting software. Each gateway's payouts must be reconciled independently. The best accounting integrations (A2X, Synder, FinTask) handle multi-gateway setups natively -- creating separate summary entries for each payment method and matching them to the correct bank deposits.

For a detailed walkthrough of connecting Shopify's default payment gateway to your accounting, see our Shopify QuickBooks integration guide.

The table below compares all the major Shopify integrations covered in this guide. Prices are approximate and shown in EUR where possible.

Key takeaway: There is no single "best" integration. The right choice depends on your accounting platform, order volume, number of sales channels, and whether you need inventory management alongside accounting sync. Read on for specific recommendations based on your business size.

Choosing the right Shopify integration depends on where you are in your growth journey. Here are concrete recommendations for three common scenarios.

You are a solo founder or small team processing fewer than 100 orders per month on a single Shopify store. Your accounting is in QuickBooks Online or Xero, you sell in one currency, and you use Shopify Payments as your only gateway.

Recommended stack:

• Accounting: Shopify Connector by Intuit (free, QBO) or Amaka (free tier, Xero/QBO)
• Inventory: Shopify's built-in inventory tracking is sufficient at this scale
• Payments: Shopify Payments only -- no multi-gateway complexity

Total cost: EUR 0/month.

At this stage, your priority is getting data into your accounting software without manual entry. The free tools handle the basics. Upgrade when you exceed 100 orders/month, add a second sales channel, or start selling in multiple currencies.

You are processing 100--1,000 orders per month, selling on Shopify and possibly Amazon or Etsy, accepting PayPal alongside Shopify Payments, and your accountant wants clean per-payout reconciliation.

Recommended stack:

• Accounting: A2X (from EUR 19/month) for per-payout accounting in Xero or QBO, or Synder (from EUR 20/month) if you need multi-platform consolidation
• Inventory: Trunk (~EUR 35/month) if you sell on multiple channels and need quantity sync; otherwise Shopify's built-in tracking is still viable
• Payments: Your accounting integration (A2X or Synder) handles Stripe and PayPal reconciliation

Total cost: EUR 20--55/month.

This is the sweet spot where a proper accounting integration pays for itself within the first month. The time saved on manual reconciliation alone (typically 3--5 hours per week) far exceeds the subscription cost.

You are processing 1,000+ orders per month across multiple channels, dealing with multiple currencies, managing physical inventory across warehouses, and your finance team needs audit-ready books with automated workflows.

Recommended stack:

• Accounting: A2X (EUR 59--99/month) or Webgility (EUR 99--249/month, QBO only) for deep accounting automation
• Inventory: Katana (from EUR 129/month) for manufacturing, or Cin7 (from EUR 349/month) for enterprise multi-channel inventory management
• AI automation layer: FinTask for intelligent reconciliation, anomaly detection, and automated categorisation on top of your existing integration stack
• Payments: Multi-gateway reconciliation handled by your accounting integration plus FinTask's anomaly detection

Total cost: EUR 150--500+/month depending on inventory needs.

At this scale, the cost of errors and manual processes dwarfs the subscription fees. A single undetected duplicate payment or missed VAT filing costs more than a year of integration subscriptions. Invest in the full stack and let your finance team focus on analysis rather than data entry.

Answers to the most common questions about Shopify integrations for accounting and automation.

The right Shopify integrations transform your store from a manual bookkeeping headache into an automated, accurate, and audit-ready operation. Whether you are a solo merchant using the free QuickBooks Connector or a high-volume seller running A2X, Cin7, and FinTask in parallel, the goal is the same: get your data flowing automatically so you can focus on growing your business.

If you are unsure which integrations fit your setup, or if you want to see how AI-powered automation can eliminate the manual work that even the best integrations leave behind, FinTask can help.

Try FinTask Free -- Connect Shopify to Everything and see how automated reconciliation, intelligent categorisation, and real-time anomaly detection work with your existing Shopify stack. Or see how FinTask integrates with Shopify for a full walkthrough of the connection process.

For more on connecting specific platforms, explore our guides to Shopify Xero integration, Shopify QuickBooks integration, and Shopify inventory sync.