Fix guides
When Shopify and QuickBooks disagree
20guides to the specific ways a Shopify → QuickBooks Online sync goes wrong: what the symptom looks like in your books, why it happens, and how to check and fix it by hand. Every one of them is free to read and doesn’t need the product.
Something looks wrong in QuickBooks
Start here if the numbers don't agree and you don't yet know why.
- Shopify orders missing from QuickBooksOrders exist in Shopify but not in QuickBooks Online? How to tell real gaps from payout timing, find every missing order, and record them correctly.
- QuickBooks revenue lower than ShopifyQBO shows less revenue than Shopify for the same period. The four causes - missing orders, unrecorded refund timing, fee netting, and settlement lag - and how to isolate each.
- VAT doubled on Shopify orders in QuickBooksQuickBooks shows roughly twice the VAT your Shopify orders actually charged. The tax-inclusive vs tax-exclusive cause, how to verify it order by order, and how to correct it safely.
- Shopify not syncing with QuickBooksOrders stopped flowing from Shopify to QuickBooks Online. A calm diagnostic order: connection, auth, settings, backlog - and how to verify what actually made it across.
- Shopify-QuickBooks integration not workingWhen a Shopify-QBO integration breaks, the urgent question isn't the tool - it's what your books are missing. How to measure the damage read-only before deciding to fix or switch.
- How to reconcile Shopify payouts in QuickBooks OnlineShopify payouts never equal your sales because of fees, refunds, and timing. The clearing-account method for reconciling payouts in QBO, step by step.
- Duplicate Shopify orders in QuickBooksShopify orders posted twice to QuickBooks Online overstate revenue and tax. Where duplicates come from, how to find every one, and how to reverse them without breaking history.
- Shopify refunds missing from QuickBooksRefunds issued in Shopify but never posted to QBO leave revenue and sales tax overstated. Why refunds are the most-dropped transaction type and how to catch every one.
- Shopify payout doesn't match the QuickBooks depositThe Shopify payout amount and the deposit in QuickBooks disagree. How fees, refunds, batching, and upstream sync errors each move the number, and how to trace a specific payout to the penny.
- Sales tax doubled on Shopify orders in QuickBooksQuickBooks shows more sales tax than Shopify collected. The two mechanical causes - tax-inclusive amounts re-taxed and duplicated orders - and how to verify which one you have, order by order.
- Shopify-QuickBooks connector migration problemsMigrated to a new Shopify-QuickBooks connector and the books haven't been right since? The three damage classes a migration leaves - gaps, overlaps, and changed posting behavior - and how to audit each.
- QuickBooks amounts don't match Shopify ordersOrders synced to QuickBooks but the amounts are wrong. Discounts, tax treatment, shipping, and currency each distort amounts in a distinct way - how to tell them apart on five sample orders.
- Shopify gift card orders wrong or missing in QuickBooksOrders paid with gift cards sync wrong or not at all, and gift card sales themselves are a liability, not revenue. How gift cards break Shopify-QBO books and how to check yours.
- Shopify multi-currency orders wrong in QuickBooksOrders in a second currency post to QuickBooks at different amounts than Shopify shows, or not at all. Where conversion happens, why the numbers diverge, and how to verify a sample properly.
Do it yourself, free
The manual method, written out. No product required.
- How to export Shopify orders to CSV for reconciliationStep-by-step: export Shopify orders (and refunds and payouts) to CSV with the right columns and date handling for reconciling against QuickBooks - pitfalls included.
- How to export QuickBooks transactions to CSV for reconciliationStep-by-step: export the Shopify-related transactions from QuickBooks Online - the right report, the right columns, the right date handling - ready to diff against a Shopify export.
- How to reconcile Shopify with QuickBooks Online manuallyThe complete manual method: match Shopify orders to QuickBooks transactions line by line with two CSV exports and a spreadsheet - counts, references, amounts, refunds, and what to do with each finding type.
Deciding what to use
Honest comparisons, including the cases where the answer isn't us.
- A2X vs the official QuickBooks connector for ShopifySummary posting vs per-order posting is the real difference between A2X and the official Shopify-QuickBooks connector. A factual comparison, who each suits, and how to verify whichever you choose.
- Do you need a bookkeeper or software for Shopify books?Bookkeeper, sync software, or both for Shopify-QuickBooks books? What each actually does, where each fails, and an honest decision framework by volume and complexity.
- Free ways to check Shopify-QuickBooks discrepanciesEvery genuinely free method for finding Shopify-QuickBooks discrepancies: built-in reports, CSV spot-checks, the full manual diff, and free scan tools - with what each can and can't catch.
Or just check your books
The free scan diffs your Shopify orders against QuickBooks line by line and tiers every finding by confidence. Two CSV exports, no account, no connection.
Scan your real books - free