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Managing your finances with Shopify can be complicated. With Shopify Payments, third-party apps, discount codes, and multi-currency orders, it’s hard to get a clear picture of your numbers. Our bookkeeping services for Shopify sellers provide accurate and organized financial records that reflect how your store operates.
We are led by a CPA and IRS Enrolled Agent. Our team does more than just data entry; we handle costs of goods sold (COGS), sales tax, and reporting from multiple channels. We speak the language of Shopify, not just spreadsheets.
2000 +
Happy Clients
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Years in industry
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Strong team
Bookkeeping for Shopify involves more than just tracking sales. It includes reconciling payment gateways, managing refunds and discounts, calculating sales tax, and tracking inventory costs. Many store owners try to handle this on their own, but they often waste time and end up with inaccurate records. Here's what we can help with.
Problem: Hiring and retaining in-house bookkeepers gets more expensive every year.
Fix: A dedicated Shopify bookkeeping team for a predictable flat fee, no hiring, no turnover.
Problem: Standard bookkeeping doesn't account for how Shopify actually works.
Fix: Shopify-specific expertise, gateways, apps, and workflows handled correctly from day one.
Problem: Multi-jurisdiction sales tax filings are easy to get wrong, and costly when you do.
Fix: We calculate, file, and remit sales tax accurately, everywhere you're obligated.
Problem: Inventory costs and profitability are hard to track with any precision.
Fix: SKU-level COGS and inventory accuracy, so your margins reflect reality.
Problem: Hours go into data entry instead of growing your store.
Fix: Automated integrations mean less manual work and more time for the business.
Problem: Monthly or quarterly reports arrive inconsistently, if at all.
Fix: Complete financials delivered on a fixed, predictable schedule.
Problem: Incomplete or inaccurate bookkeeping means you can't trust your reports.
Fix: Clean, reconciled books you can act on without second-guessing.
Problem: Poor integration between Shopify and QuickBooks or Xero creates constant cleanup.
Fix: Seamless integration, so data flows automatically, no CSV imports, no cleanup.
Bookkeeping for Shopify involves more than just tracking sales. It also includes managing payment gateways, refunds, discounts, and inventory all at the same time. Our team focuses on Shopify to handle these tasks for you.
Every order batch tied to bank activity and the general ledger, gross sales, discounts, shipping, taxes, and gift cards reconciled with a clear trail, not bulk month-end entries.
Payouts from Shopify Payments, Stripe, and PayPal matched to orders, with fees, refunds, and disputes posted to the right accounts.
SKU-level costing using FIFO or weighted average, so receipts, adjustments, and write-offs keep your margins accurate and readable.
Sales tax mapped correctly, filing calendars tracked, and reports prepared to match your obligations state by state, country by country.
Vendor bills captured, coded, and matched to purchase orders, so recurring costs stay predictable, and cash flow stays clear.
Shopify plus Amazon, eBay, or Walmart consolidated into one consistent chart of accounts, with FX gains and losses tracked clearly.
P&L, balance sheet, and cash flow with net sales, returns, AOV, and product-level trends, not generic statements you can't act on.
Contractors and staff recorded correctly, with payroll summaries tied to your bank and GL, and employer taxes posted where they belong.
Clean setup with QuickBooks, Xero, NetSuite, or A2X, so entries land in the right accounts automatically, no manual imports.
We start by digging into your store's setup, payment gateways, apps, discount codes, and inventory tracking to see where the numbers stop lining up. We surface what's broken before it costs you more.
We tie every order to your bank activity and general ledger, set up SKU-level COGS tracking, and integrate your Shopify store directly with QuickBooks, Xero, or NetSuite, so entries land in the right accounts automatically.
We map your sales tax obligations across every state and country you sell in, and consolidate any other channels, Amazon, eBay, Walmart, into one clean, unified set of books.
You get up-to-date dashboards on cash flow, margins, and product performance, plus a dedicated point of contact, so you always know your numbers and can plan your next move with confidence.
CFO | IRS Enrolled Agent
Gary started Ledger Labs in 2014 and has helped over 2,000 ecommerce businesses improve their finances. He focuses on CFO services, setting up ERP systems such as NetSuite, Odoo, and QuickBooks, and automating financial processes for growing online brands.
Operations Manager
Allison is a Certified Public Accountant (CPA) and a member of the AICPA. She oversees operations at Ledger Labs, ensuring accurate, compliant financials for hundreds of clients. With experience in both public and private accounting, she builds scalable systems that support fast-growing ecommerce businesses.
Accountant
Matt brings 7+ years of accounting experience across ecommerce, SaaS, and technology. He specializes in financial reporting, month-end close management, and ERP implementations (including NetSuite transitions). Matt ensures our clients get accurate, timely financials they can rely on for growth decisions.
Many Shopify sellers seek our help after a generalist bookkeeper combines their payment gateways, discounts, and refunds into one confusing line. This process makes it hard for them to see their true profit margins.
| Feature | Ledger Labs’ Bookkeeping Services for Shopify Sellers | Other Services |
|---|---|---|
| Order to GL Reconciliation | Every Shopify order batch ties to bank activity and the general ledger. Gross sales, discounts, shipping income, taxes, fees, and gift cards reconcile to Shopify reports with a clear trail. | Month end bulk entries based on deposits. Discounts, shipping, and fees grouped together. Variances appear with no reliable link back to orders. |
| Payment Gateway Payouts | Payouts from Shopify Payments, Stripe, PayPal, and other gateways matched to orders. Fees, refunds, disputes, and reserves posted to the right accounts. Balances agree to statements. | Deposits booked as income on receipt. Fees estimated later. Suspense accounts grow and require cleanup during close. |
| Sales and Revenue Tracking | Revenue segmented by product group, variant, channel, and promotion. Gross, returns, and net shown separately so trends are easy to read. | Single revenue line. Returns and promotions distort totals. Trend reviews require manual spreadsheets. |
| Refunds, Discounts, and Chargebacks | Refunds link to the original sale with tax and COGS reversals when applicable. Discount codes tracked. Chargebacks posted with related fees and tied back to the order. | Refunds posted as negative sales only. Taxes and COGS reversals missed. Disputes recorded as generic bank expense. |
| Inventory and COGS Accuracy | SKU level costing using FIFO or weighted average as selected. Receipts, adjustments, and write offs tie to sub ledgers and the GL so margins remain readable. | COGS set from rough percentages. Unit costs drift. Inventory and GL do not match at close. |
| Expense and Vendor Management | Vendor bills captured, coded, and matched to purchase orders or receipts. Recurring costs reviewed so cash outflows stay predictable. | Bills entered without matching or coding standards. Recurring costs fluctuate. Forecasting remains unclear. |
| Sales Tax and Compliance | Sales tax mapped to liability accounts. Filing calendars tracked. Reports prepared to match portal totals for each state or country. | Sales tax held in revenue or posted loosely. Filing numbers do not match collections. Notices and penalties become common. |
| Multi Channel Consolidation | Shopify plus marketplaces like Amazon, eBay, Etsy, or Walmart consolidated with a consistent chart of accounts. Channel views remain available for reviews. | Separate files per channel with inconsistent coding. Roll ups require manual work each month. |
| Multi Currency and FX | Foreign currency sales and payouts translated with recorded rates. FX gains and losses posted clearly so product margins remain readable. | Foreign activity booked at deposit value only. FX differences hidden in miscellaneous expense. |
| Financial Reports and Insights | P and L, balance sheet, and cash flow with supporting schedules. Views for net sales, returns, discounts, contribution margin, AOV, and product or channel trends. | Generic statements with limited detail. Changes are hard to explain. Decisions rely on guesswork. |
| Cash Flow Visibility | Collections, payouts, inventory buys, and operating spend shown by week and month. Owners can see when cash tightens and why. | Payouts treated as income. No timing view on holds or reserves. Cash surprises near payroll or tax dates. |
| Integrations and Setup | Clean mappings with Shopify and tools like QuickBooks, Xero, NetSuite, and A2X. Entries land in the right accounts on first pass. Exceptions reviewed and corrected. | CSV imports without controls. Data posted to catch all accounts. Cleanup required at close. |
| Month End Close and Audit Trail | Bank, gateways, inventory, receivables, payables, and tax reconciled. Source files attached. Reviews logged so handoffs remain smooth. | Ad hoc close in spreadsheets. Limited backup for entries. Rework increases at year end. |
| Payroll and Team Payments | Contractors and staff recorded correctly. Payroll summaries tie to bank and GL. Employer taxes and benefits posted to the right cost centers. | Lump sum payroll and contractor entries. Taxes and benefits posted later. Cost centers lack accuracy. |
| Dedicated Support | One point of contact who knows your Shopify setup, flags issues early, and schedules reviews so owners have clear next steps. | Ticket queue with rotating staff. Context gets lost between messages. |
| Flat Monthly Pricing | One predictable monthly fee covers Shopify bookkeeping, reconciliations, close support, and reporting. No surprise add ons. | Hourly billing and per task adders. Costs rise when you ask for help. |
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I had trouble figuring out which payouts from Shopify Payments, Stripe, and PayPal matched my orders. Ledger Labs connected each payment gateway to my actual sales, including the fees. Now, my financial records balance, and I no longer have to guess at the end of each month.
Tobias Renwick Founder