Collect a W-9 from every subcontractor before you issue the first payment. Not after the first invoice. Not in January when you’re scrambling to file. Before you pay them anything. Make it part of your onboarding alongside the signed subcontract and insurance certificates. Store the W-9s digitally so you have the legal name, address, and tax ID ready when filing season arrives.

In QuickBooks Online, create a vendor record for each sub and enter the information from their W-9. Check the box that marks them as a 1099 vendor so QBO automatically tracks their total payments throughout the year. This takes a couple of minutes per sub and eliminates the January panic of chasing down tax IDs from people who may not return your calls.

Every payment to a sub needs to hit the correct project. If you’re running multiple jobs, a lump “subcontractor expense” account tells you nothing useful. Set up each project in QBO and assign sub invoices to the appropriate job when you enter them. This is the foundation of construction job costing and it’s how you know whether a project is actually profitable or just feels profitable because revenue is coming in.

Retainage requires its own tracking. When a sub invoices $10,000 and you hold 10% retainage, you pay $9,000 and record the remaining $1,000 as retainage payable. The full $10,000 hits the project cost when the work is performed, which keeps your job cost reports accurate. When you release the retainage after final inspection or project completion, you pay against that liability. If you just short-pay invoices without tracking retainage separately, your project costs will be understated and you’ll lose visibility into what you actually owe.

For 1099-NEC filing, any subcontractor you pay $600 or more in a calendar year must receive a 1099-NEC. The deadline to both file with the IRS and furnish copies to the subcontractor is January 31. If your vendor records are set up correctly and marked as 1099 eligible, QBO can generate and e-file them directly. The process is straightforward when the data is clean. It becomes a nightmare when vendor records are incomplete or payments weren’t coded properly.

The penalties for not filing are real. The 2024 rate is $310 per form you fail to file on time. For a general contractor working with 20 or 30 subs, that adds up to thousands of dollars for something that takes a few hours if your books are maintained throughout the year. If the IRS decides you intentionally ignored the requirement, there is no cap on the penalty amount.

One thing that trips up a lot of contractors is paying a sub through a personal account or cash and forgetting to record it. That payment still counts toward the $600 threshold, and the IRS can still penalize you for not reporting it. Run every sub payment through your business account so there is a clear trail. Having construction bookkeeping services handle this monthly means your vendor records stay current and nothing falls through the cracks at year-end.