Fix guide
Free ways to check Shopify-QuickBooks discrepancies
You suspect your Shopify books are off and you'd rather verify before spending anything. Reasonable - and genuinely possible. Everything on this page is free, including the honest observation that the manual methods work and simply cost your time instead of money.
One of the options below is ours (LedgerClear's free scan - actually free, no card, works on CSV exports without connecting anything). We've listed it alongside the manual methods with the same plain accounting of what it catches and what it doesn't, because the right choice depends on how deep you need to go and how much time you have.
The methods stack: start with the five-minute checks, and only escalate to the deeper ones if something smells wrong.
The symptoms
- A number feels off - P&L, tax liability, a payout - but you haven't confirmed anything yet
- You want a periodic health check on your sync without a subscription
- You're deciding whether professional cleanup is worth it and want to see the damage first
- You've been burned by a sync before and trust nothing without verification
Why it happens
Level 1 - free five-minute checks with built-in reports
Count comparison: paid orders in Shopify admin vs. sales transactions in QBO for the same settled month (exclude the last ~5 business days for settlement). Total comparison: Shopify's sales report (gross, refunds, net separately) vs. your QBO income and contra-revenue accounts. Tax comparison: Shopify's tax report vs. QBO's tax liability report. Any of the three disagreeing tells you a discrepancy exists - none of them tells you which orders. Cost: free. Catches: that something is wrong. Misses: what.
Level 2 - free targeted spot-checks
Sample five orders of each risky shape - around a migration date, with a discount, paid by gift card, in a foreign currency, with a partial refund - and trace each into QBO by order number. Ten to fifteen minutes, and because failure classes are systematic, one bad sample order usually reveals a rule that's wrong across your whole history. Catches: the mechanism. Misses: the full list of affected orders.
Level 3 - the full diff, manual or scanned
The complete answer is a line-by-line diff of every order and refund. Free option A: do it yourself with two CSV exports and a spreadsheet - our manual reconciliation guide is the full method; budget a few hours. Free option B: upload those same two CSVs to LedgerClear's free scan and get the same diff in about a minute, findings tiered by confidence (confirmed / likely timing / needs review), read-only, no card, no connection required. Both produce the thing the quick checks can't: an itemized findings list. The paid part of LedgerClear - proposed correcting entries - only matters if the free diff finds damage you'd rather not fix by hand.
How to check and fix it by hand
- 01
Run the three report comparisons
Counts, totals, tax - Shopify vs. QBO for one settled month, buffer excluded. All three matching is a genuinely good sign (though it can't rule out offsetting errors). Any mismatch: continue.
- 02
Spot-check the risky shapes
Five orders per risky category, traced by order number into QBO. Note which category breaks - that's your failure mechanism, and it tells you what the full diff will find at scale.
- 03
Run the full diff
Manual (spreadsheet, a few hours, full control) or LedgerClear's free scan (same CSVs, about a minute). Either way, the output you want is a findings list: this order missing, that one duplicated, these amounts wrong, those refunds unrecorded.
- 04
Then decide about money - with the facts in hand
A clean diff: keep the free checks as a monthly habit and spend nothing. A findings list: now you're choosing between your own hours, your bookkeeper's rate, or a paid cleanup - with the damage itemized, whichever path prices honestly. Never pay to find out whether something is wrong; finding out is free.
Common questions
- Is there a truly free way to check Shopify against QuickBooks?
- Yes - three, stacking by depth: built-in report comparisons (five minutes, detects that something is off), targeted spot-checks by order number (fifteen minutes, finds the mechanism), and a full line-by-line diff via spreadsheet or LedgerClear's free CSV scan (itemizes every finding). All genuinely free.
- What's the catch with LedgerClear's free scan?
- The scan itself is complete - full diff, all findings, confidence tiers, no card. The business model: if the scan finds damage, fixing it is where paid cleanup (proposed correcting entries you approve individually) is offered. You can take the free findings list to your own bookkeeper instead; it's built to be useful either way.
- How often should I run a free check?
- Monthly report comparisons take five minutes and catch drift early; a full diff quarterly, after any sync migration or outage, and before tax filings. Discrepancies get harder to correct once periods are filed, so checking beats discovering - see our migration and manual reconciliation guides for the deeper passes.
LedgerClear doesn’t replace your sync. It audits per-order syncs today - the official connector and Synder. Summary-posting tools like A2X and Link My Books: auditing support is coming later, and LedgerClear runs alongside them without touching their entries. If the right answer for you is switching tools, the scan report is the damage report to migrate with.