thread Re: In payroll I select write manual check, but discovered that for last 6 months Square also deduct in Staff & Payroll

In payroll I select write manual check, but discovered that for last 6 months Square also deducting

C3rp3nt3r — Wed, 11 Mar 2026 05:22:51 GMT

In payroll I select to write manual check. Just discovered that for last 9 months Square has been deducting amount from my bank account that matches the check I wrote. Employee never input bank info for direct deposit.

Re: In payroll I select write manual check, but discovered that for last 6 months Square also deduct

Stacelyn24 — Wed, 11 Mar 2026 18:07:14 GMT

That definitely sounds worth looking into a little deeper, because when I’ve used manual check in Square Payroll, my understanding has always been that I’m responsible for issuing the check myself, while Square still withdraws payroll taxes and related liabilities separately — not the employee’s check amount as a second payment.

A couple of things I’d want to confirm: when the money was withdrawn, was it showing as payroll taxes only, or the full employee net pay amount? And under your payroll settings, is there any chance direct deposit was still enabled at the company level even if the employee never entered bank details? If the withdrawal is matching exactly what you wrote manually, I’d definitely recommend contacting Square's customer support at 1-855-700-6000 so they can review the payroll records and tell you exactly where those funds were routed.

Re: In payroll I select write manual check, but discovered that for last 6 months Square also deduct

perkits — Wed, 11 Mar 2026 18:28:43 GMT

Yes I would call Payroll Support. I think I would have noticed this after 1 payroll.

Re: In payroll I select write manual check, but discovered that for last 6 months Square also deduct

C3rp3nt3r — Sun, 15 Mar 2026 01:22:30 GMT

Thanks, Ill contact them.

Re: In payroll I select write manual check, but discovered that for last 6 months Square also deduct

C3rp3nt3r — Sun, 15 Mar 2026 01:25:44 GMT

My fault not monitering my bank acct more closely, but was fine before. Confusing why this started about a month ago. Will definitely make the call. Thanks