Pay Contractors in QuickBooks Without the Manual Work

Cleo Pay collects the W-9, runs the approval, sends the ACH payment, and writes every contractor payment back to QuickBooks Online against the right vendor and account. Your 1099 data is current all year, not reconstructed in January.

Book a DemoSee how the sync works

Two-way sync with QuickBooks Online. Contractors onboard themselves in under a minute.

Cleo Pay accounting settings with QuickBooks connected, auto-create vendors and auto-create bill payments enabled, and invoice sync status

How it works

Three steps, then it runs itself

The manual part of paying contractors is not writing the check. It is collecting the W-9, chasing the invoice, coding it correctly, and then typing the whole thing into QuickBooks a second time. Cleo Pay removes all four.

  1. 01

    Invite the contractor

    Send a link, or share one QR code with a whole crew. The contractor enters their tax details, connects a bank account through Plaid, and signs their W-9. It takes under a minute and you never chase a form.

  2. 02

    Approve the invoice

    Contractors submit invoices from their own portal instead of emailing you a PDF. Smart Capture reads the amounts and line items, and you approve in one click from the dashboard.

  3. 03

    Pay and sync

    Send Standard ACH at no cost, or Fast ACH when someone needs the money sooner. The moment it clears, the payment posts to QuickBooks Online as a bill payment against the right vendor and expense account.

The sync

What moves between the two systems

RecordDirectionWhat happens
Vendors and contractorsCleo Pay to QuickBooksNew contractors are created as QuickBooks vendors automatically when you enable auto-create.
Bills and invoicesBoth directionsApproved invoices become bills. Edits made in QuickBooks flow back on the next sync.
Bill paymentsCleo Pay to QuickBooksEvery completed payment posts as a bill payment, so the bill closes and the bank line matches.
Chart of accountsQuickBooks to Cleo PayYour existing categories come across and stay mapped, so coding does not drift.
Bank accountsQuickBooks to Cleo PayMap each paying account once. Payments land against the account you expect.

What happens at 1099 time

Because the W-9 is collected before the first payment goes out, you are never reconstructing tax details in January. Cleo Pay keeps a running total for each contractor against the current 1099-NEC reporting threshold, so you can see who crosses it well before year end.

Questions

Paying contractors in QuickBooks

Can you pay 1099 contractors through QuickBooks Online?
QuickBooks Online is your accounting system, so it records contractor payments, but the work around the payment still lands on you: collecting the W-9, chasing the invoice, coding the expense, and moving the money. Cleo Pay handles that whole loop and writes the finished payment back into QuickBooks Online, so your books stay the system of record without the manual entry.
How do contractor payments show up in QuickBooks?
Each completed payment posts to QuickBooks Online as a bill payment against the contractor's vendor record and the expense account you mapped. The bill closes, the bank line matches, and there is nothing left to key in by hand.
Do my contractors need a QuickBooks login?
No. Contractors use their own Cleo Pay portal to submit invoices and track payment status, and they never touch your QuickBooks account. You keep full control of who can see your books.
How does Cleo Pay collect W-9s?
The W-9 is part of the contractor's self-onboarding, before any money moves. They open your invite link, enter their tax details, connect a bank account through Plaid, and sign, typically in under a minute. You are not emailing PDFs back and forth.
How fast do contractors get paid?
Standard ACH lands in 3 to 5 business days at no cost. Fast ACH lands in 1 to 2 business days for a fee, which is the option to use when someone needs the money before the weekend.
Does this work with QuickBooks Desktop?
The integration supports QuickBooks Online on all plans today. QuickBooks Desktop is on the roadmap, so get in touch if that is what your business runs on and we will share timing.
Can I onboard a whole crew at once?
Yes. Alongside individual email invites you can share one onboarding link or QR code with an entire crew, and each person completes their own W-9 and bank connection from it. This is the fastest path when you are bringing on many contractors at the same time.
What happens when a contractor crosses the 1099 threshold?
Cleo Pay keeps a running total for every contractor and tracks it against the current 1099-NEC reporting threshold, so you can see who is approaching it during the year instead of discovering it in January. Because the W-9 was collected up front, the year-end export already has what your accountant needs.

See a contractor payment land in your QuickBooks

We will connect a sandbox to QuickBooks Online, onboard a test contractor, and run a payment end to end so you can watch it post.

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