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Running an online store means dealing with a constant stream of financial data. Global ecommerce revenue is expected to jump by over $2 trillion between 2023 and 2027, according to Statista. For Shopify merchants, that means more transactions to track, more tax rules to follow, and more payment streams to reconcile.
Revenue flows through different sales platforms, payment processors, and apps before landing in your accounting system. Capturing every transaction correctly, no matter where it comes from, is what separates knowing your numbers from hoping they’re right.
This guide covers what Shopify bookkeeping really involves, which records matter most, and which tools can help you maintain accurate books as your store scales.
TL;DR
- Track the money that moves: Sales, fees, taxes, refunds, and COGS all need accurate recording for reliable cash flow.
- Multiple gateways complicate reconciliation: Shopify Payments, PayPal, and other processors report on different schedules and formats
- Automation fixes what manual entry can’t: Tools like Synder sync Shopify data into QuickBooks, Xero, and other platforms with real-time accuracy
- Clean inventory tracking protects margins: Accurate COGS and stock counts help you understand profitability and plan purchases confidently
What Shopify bookkeeping actually is
Unlike traditional retail bookkeeping, Shopify’s multi-channel ecosystem creates unique complications that can quickly turn clean records into a reconciliation nightmare.
Why Shopify bookkeeping is trickier:
- Fragmented payment data – Multiple gateways (Shopify Payments, PayPal, Klarna) report on different schedules and batch payments differently.
- App-driven complexity – Discount apps, subscription tools, bundling software, and loyalty programs constantly modify order values.
- Multi-jurisdictional taxes – Tax rates vary by customer location, requiring consistent tracking across regions to avoid inflated revenue or incorrect liabilities.
- Fast-moving inventory – Multiple SKUs and variants shift with every sale, return, and restock, making real-time accuracy critical.
Without proper systems in place, you’ll see different numbers depending on which report you check. A seller using three payment gateways might find deposits arriving days apart, mixed batches of orders and refunds, and totals that don’t match at first glance. That’s why structured bookkeeping is what keeps your financial data usable.
The records every Shopify seller must track
These entries determine how you see revenue, understand tax obligations, and manage cash flow. When tracked consistently, reconciliation and reporting become far less painful.
Sales and order details
Orders need to show what was sold, the price, any discount, and taxes collected. A $40 order with a 10% discount and $3.20 in tax needs each piece recorded separately. Otherwise, your revenue and tax reports stop being reliable.
Payment gateway fees
Every processor subtracts fees before sending money to your bank. A $100 PayPal order might arrive as $96.40, and that $3.60 fee needs recording to keep your margins accurate.
Sales tax collected
Tax rates vary by state and country. If you sell the same product to customers in New York and Texas, for instance, you should be charging different tax amounts. Capturing those details from the start means no scrambling at tax season.
Refunds and chargebacks
Refunds affect taxes, fees, and inventory counts. You need to account for the revenue reversal, tax adjustment, and potentially processing fees if your processor doesn’t return them.
Cost of goods sold and inventory changes
Every sale should reduce your stock count and increase COGS based on what you paid for the item. Let’s say you sell three units at $12 each. Then your system should reduce inventory by three units and increase COGS by $36.
Expenses
App subscriptions, shipping tools, marketing campaigns, packaging materials – categorizing them properly helps you understand where money goes and identify areas to cut costs.
Once you know what records matter, the next question is where to keep them. The right accounting software makes tracking these transactions far easier, but only if it matches how your store actually operates.
How to keep records accurate: the data problem
Knowing what to track is one thing. Actually keeping those records accurate is another. Tracking all those transactions manually is nearly impossible once your store scales. Manual entry means hours of work every week and errors that compound month after month.
That’s why you need automation tools like Synder. Synder gathers transaction data from both your Shopify store and the payment processors you’re using: Shopify Payments, PayPal, Stripe, and 30+ other platforms.
The data Synder captures includes:
- Order details: sales, discounts, taxes, shipping, coupon names
- Payment gateway fees for each processor
- Payout breakdowns that match bank deposits
- Refund components: revenue reversals, fee adjustments, tax corrections
- Inventory changes from sales and returns
- Gift cards, Shop Cash, and other Shopify-specific transactions
What this solves for Shopify sellers: Synder separates mixed transactions into clean categories, reconstructs payouts to match deposits, handles multi-gateway complexity, and keeps inventory and COGS synced automatically. Instead of spending hours matching transactions manually or dealing with mismatched deposits, you get organized data that reconciles cleanly.
Synder prepares all this transaction data and pulls it as clean, structured, and detailed entries directly into your accounting software.
Get your Shopify bookkeeping under control. Try Synder free or book a demo to walk through your specific setup.
Shopify bookkeeping software: 4 options compared
Shopify sellers use everything from lightweight tools to full ERPs. Here’s what each platform offers and where it fits.
QuickBooks Online + Synder
QuickBooks Online is a cloud-based accounting platform popular with small and midsize businesses. It covers invoicing, expense tracking, bank connections, tax management, and financial reporting.
Synder automates your Shopify-to-QuickBooks sync, handling transaction breakdowns, payment gateway fees, and payout matching automatically.
QuickBooks key features:
- Automated bank feeds that pull transactions from connected accounts
- Invoicing tools for creating and tracking payments
- Expense tracking with mobile receipt capture
- Standard financial reports (P&L, cash flow, expense summaries)
- Basic inventory management on select plans
Best for: Small to mid-size Shopify stores with moderate order volumes, straightforward inventory, and uncomplicated cash flow. Works particularly well for U.S.-based businesses.
Pricing:
| Plan | Price | What you get |
| Simple Start | $38/mo | Basic accounting for one user: income/expense tracking, bank connections, invoices, basic reports |
| Essentials | $75/mo | Adds bills, bill-pay, vendor management, time tracking, and multiple users |
| Plus | $115/mo | Adds inventory, projects/job costing, budgeting, and stronger reporting |
| Advanced | $275/mo | Advanced reporting, automation, workflows, analytics, custom roles, higher user capacity |
Xero + Synder
Xero is also a cloud-based platform, which is built around simplicity and team collaboration. This platform is used by small businesses and ecommerce sellers who need solid accounting without the weight of a full ERP.
Synder keeps your Xero data clean by pulling structured Shopify transactions directly into your books.
Xero key features:
- Unlimited users across all plans
- Bank feeds with automated reconciliation
- Multi-currency support on higher-tier plans
- Core accounting tools: invoicing, expense tracking, financial reporting
Best for: Small to medium Shopify stores that need flexibility without excessive complexity, especially those with multiple team members or occasional international sales.
Pricing:
| Plan | Price | What you get |
| Early | $20/mo | Very small businesses: limited invoices and bills, basic reconciliation |
| Growing | $47/mo | Unlimited invoices, bills, bank reconciliation, core accounting features |
| Established | $80/mo | Adds multi-currency, expenses, projects, analytics, advanced features |
Oracle NetSuite + Synder
Oracle NetSuite is a comprehensive cloud ERP that goes beyond basic accounting. It combines financial management, inventory and order processing, CRM, supply chain operations, and multi-entity capabilities into one system built for larger or more complex businesses.
Synder uses the Summary Sync mode to handle high transaction volumes without cluttering NetSuite, consolidating Shopify activity into clean batch journal entries.
NetSuite key features:
- Full financial management: GL, AP/AR, cash flow, multi-entity consolidation, multi-currency, fixed assets, reporting
- Inventory, order, and warehouse management with stock control and fulfillment tracking
- Integrated CRM and billing that connects customer orders to revenue recognition
- Real-time dashboards across finance, operations, inventory, and customer data
Best for: Mid-size to large ecommerce brands managing multiple sales channels, high order volumes, and complex inventory across multiple warehouses or locations. Works well for companies operating across different legal entities, currencies, or countries.
Pricing:
| Component | Price | Notes |
| Base license | Starts $999/mo | Core ERP platform; varies by edition |
| User licenses | Starts $99/user/mo | Per-user pricing; varies by role and access |
| Modules | Varies | Add-ons like Advanced Inventory, WMS, CRM |
Sage Intacct + Synder
Sage Intacct is a cloud-based, finance-focused ERP with strong core accounting: GL, AR/AP, cash flow management, multi-entity consolidation, and advanced reporting. Sage is well suited for growing businesses that need reliable financial operations and multi-entity or multi-currency support without the broader supply-chain or warehouse modules found in full operational ERPs.
Synder’s Summary Sync mode keeps Sage Intacct organized by rolling up Shopify transactions into aggregated entries – perfect for businesses processing thousands of orders without overwhelming your general ledger with individual line items.
Sage Intacct’s key features:
- Core financial modules: GL, AP/AR, cash management, fixed assets, multi-entity consolidation, multi-currency, advanced reporting
- Dimensional reporting: track performance by entity, department, project, or product line
- Integrations with inventory or order systems for flexible setups
- Strong compliance and accounting workflows
Best for: Mid-size and growing ecommerce brands operating across multiple entities, revenue streams, or countries, but don’t require complex supply-chain or warehouse management. Good for companies needing consolidated financial statements for investors, audits, or internal controls.
Pricing:
| Component | Price | Notes |
| Base subscription | ~$12,000–$35,000/year | Core financials; pricing depends on configuration, entity count, and user licenses |
| Users | Additional cost | Varies by user type (business user vs. employee user) |
| Modules | Additional cost | Add-ons like Contracts, Multi-Entity, Revenue Management, Projects, Inventory can add $3,000–$10,000+/year |
How to choose the right fit
The software that works for a 5-person startup won’t make sense for a multi-entity brand doing $50M in revenue. Match your choice to both your current reality and where you’re headed in the next 2-3 years.
| If your store… | Consider |
| Is small or mid-sized, with limited SKUs, simple inventory, and few payment gateways | QuickBooks Online or Xero – affordable, simple, easy setup |
| Has modest growth, multiple users or international customers, but operations remain fairly simple | Xero – simplicity & unlimited users, or QuickBooks Online – more features or if U.S.-based |
| Is growing fast, needs financial consolidation, multiple entities/currencies or strong reporting, but doesn’t need warehouse-level complexity | Sage Intacct – strong accounting, good for growth, flexible integrations |
| Has complex inventory, multiple sales channels, warehouses, global customers, and needs end-to-end system covering orders → inventory → accounting → CRM | Oracle NetSuite – full ERP, unified operations, scalable but expensive |
Best practices for smoother Shopify bookkeeping
Good software helps, but it’s your daily habits that keep the books clean. These seven tips prevent the most common bookkeeping mistakes.
1. Keep a consistent chart of accounts
Use the same income, fee, discount, and COGS accounts every time. When categories shift between months or duplicate accounts appear, your financial reports become unreliable and trend analysis falls apart. A stable chart of accounts gives you cleaner statements and makes it far easier to spot problems early.
2. Give each payment gateway its own clearing account
Shopify Payments, PayPal, Amazon Pay, and Klarna should each flow into separate clearing accounts. Mixing payment gateways in one account makes payouts nearly impossible to match and creates reconciliation nightmares. Separate accounts mean you can track each processor’s fees accurately and reconcile deposits without sorting through mismatched batches.
3. Keep taxes separate from revenue
Sales tax belongs in a liability account, not in revenue. This mistake inflates your revenue numbers and creates tax filing problems. When tax amounts vary across channels and aren’t tracked consistently, you end up with incorrect liability totals and potential compliance issues. Proper separation makes tax filing smoother and keeps your revenue reporting honest.
4. Track inventory updates with every transaction
Ignoring inventory changes causes inaccurate COGS and drifting stock levels. Every sale should reduce inventory and increase COGS. Every return should reverse those entries. When this connection breaks down, your profit margins become unreliable and you lose visibility into what you actually have in stock. Clean inventory tracking protects your margins and prevents stockouts or overordering.
5. Record refunds and chargebacks completely
Refunds do more than reverse revenue. They affect taxes, fees, and inventory counts. Many sellers only record the revenue reversal and miss the fee adjustments or tax corrections. Recording all three components (revenue, fees, taxes) shows what actually happened and keeps profitability realistic. Missing these details distorts your financial picture.
6. Reconcile weekly, not monthly
Weekly reconciliation helps you spot mismatched dates, grouped payouts that don’t align with orders, and missing fee data before they pile up. Waiting until month-end means small problems compound into hours of detective work. Catching discrepancies early speeds up the month-end close and reduces surprises.
7. Automate to implement these practices consistently
Tools like Synder enable you to implement all these practices automatically. Manual processing during high-volume periods creates duplicate entries, incomplete fee data, and inconsistent formats between channels. Automation standardizes your data before it hits your accounting software, eliminating the most common sources of bookkeeping errors, keeping your financial records reliable and saving you up to 120 hours a month.
The bottom line: What you should know about Shopify bookkeeping
The stakes with Shopify bookkeeping are higher than most sellers realize. Bad books don’t just complicate tax season but hide cash flow problems, mask unprofitable products, trigger incorrect sales tax filings, and create audit exposure that can cost thousands to fix.
Here’s what matters: QuickBooks, Xero, NetSuite, and Sage Intacct all handle standard accounting well, but none can fix fragmented Shopify data on their own. When payment processors report differently, apps modify transactions, and deposits don’t match orders, your accounting platform just imports the chaos. Automation tools like Synder solve this by standardizing the mess before it reaches your books, separating gateway fees, reconstructing payouts accurately, and syncing inventory changes in real time.
Start with the basics: pick accounting software that matches your complexity level, set up separate clearing accounts for each payment gateway, and automate your data flow from day one. The time you save on reconciliation and month-end close pays for itself, and the difference in data reliability shows up immediately in every financial decision you make.
FAQ
Does Shopify have built-in accounting software?
No. Shopify provides sales reports and basic financial tracking, but you need dedicated accounting software like QuickBooks Online, Xero, Sage Intacct or NetSuite for complete bookkeeping, expense tracking, and tax compliance.
How does Shopify bookkeeping work?
Shopify bookkeeping tracks sales, fees, taxes, refunds, inventory, and payouts, recording them accurately in accounting software. This keeps financial data consistent and matched to bank deposits for proper reconciliation.
Do I need a bookkeeper for my Shopify store?
Small stores can start with DIY bookkeeping, but as transaction volume grows, hiring a specialized Shopify bookkeeper saves time, ensures accuracy, and prevents costly tax mistakes or compliance issues.
What’s the best accounting software for Shopify?
QuickBooks Online and Xero work best for most sellers. Sage Intacct fits multi-entity brands. NetSuite suits large operations. Pair these with automation tools like Synder for clean data.
How do I track sales tax on Shopify?
Shopify calculates tax at checkout. Track where you have nexus, ensure correct rates apply, and use bookkeeping tools to keep tax records accurate and organized for filing deadlines.
How do I calculate COGS for Shopify products?
Sum direct costs (product purchase price, manufacturing, shipping to you) for items sold during the period. Update COGS with every sale or return to maintain accurate profit margins.
