Quickbooks Tips For Square Users
- JoAnne Lutat
- 14 hours ago
- 2 min read

Many small business owners love Square because it makes taking payments simple. But sometimes the Square and QuickBooks integration can be glitchy and create confusion when the numbers don’t match.
I worked with a client recently who was experiencing exactly this problem. Their QuickBooks income never seemed to match the Square reports, even though everything looked correct at first glance.
If you’re using Square and QuickBooks together, here are a couple of common reasons this happens.
Square Deposits Are Net of Fees
When Square deposits money into your bank account, the amount is not the total of what customers paid.
Square subtracts things like:
Processing fees
Refunds
Discounts or comps
Adjustments
So the deposit you see in your bank account is the net amount.
But your accounting system should record the whole sale first, then track the fees separately.
Additionally, when deposits are posted directly to income (which happens when you add them from your banking screen,) QuickBooks ends up recording net sales instead of gross sales, which makes your reports inaccurate.
There's usually a time difference between the sale and the deposit, which throws your numbers off.
Why These Cause Problems
When sales are recorded as net deposits, and when deposits are recorded days after the sale:
Your income may appear higher or lower than it really is
Processing fees may not be clearly tracked
Reports may not match Square sales summaries
Reconciling accounts becomes frustrating
Over time, these can make it difficult to trust your financial reports.
The Simple Workflow That Usually Fixes It
The most reliable solution is using a Square clearing account in QuickBooks. This account temporarily holds the sales before the actual deposit reaches the bank.
Here’s how that works in simple terms:
Square sales are recorded to the clearing account
Square fees are recorded separately as expenses
The actual bank deposit clears the remaining balance
When set up properly, this allows:
Square reports
QuickBooks income
Bank deposits
to all line up correctly.
A Quick Reminder
The Square integration can work well, but it often needs a little adjustment to the workflow to keep everything accurate.
If your QuickBooks income never seems to match your Square reports, you're definitely not alone. It’s one of the most common bookkeeping issues I see with small businesses.
Thankfully, it’s usually an easy fix once the system is set up correctly.
—JoAnne Lutat
BlancoDev Bookkeeping
Helping small businesses keep their numbers clear and reliable.

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