Contractor 1099s

When you pay a freelancer or other independent contractor (someone who is not your employee) for work for your business, the IRS usually wants you to report it on Form 1099-NEC (“nonemployee compensation”). You send one copy to the IRS and one to the contractor. Bokapsys works out who needs one and how much to report, builds each form, and prepares the CSV file that the IRS’s free IRIS website (Information Returns Intake System) accepts. You upload it yourself.

Caution

Bokapsys does not send anything to the IRS. It prepares the forms and the upload file; you upload the file on the IRS website and give each contractor their copy, then record in Bokapsys that you filed.

1. 1Mark contractors
2. 2Record payments
3. 3Create 1099 forms
4. 4Download the IRIS file
5. 5Upload at IRS IRIS
6. 6Mark as filed

Who gets a 1099-NEC in Bokapsys

Bokapsys prepares a 1099-NEC for someone when all of these are true:

1. They are one of:
   • a vendor ticked Send this contractor a 1099 on their vendor page (most vendors, companies you buy goods from, don’t need one, so this is off by default), or
   • a contractor under Payroll → People with Gets a 1099-NEC at year end ticked (it is ticked for a new contractor), whose payments you record on their page. See Contractors.
2. You paid them at least $2,000 in the tax year (the 2026 reporting threshold).
3. Their full nine-digit tax ID is on file.

Cash basis: what counts as “paid”

A 1099 reports money you actually paid in the calendar year, not bills you received. Bokapsys adds up, by the date of each payment:

• for a vendor, the payments you recorded with Record payment on their bills under Invoicing (AP-AR) → Bills, once settled;
• for a payroll contractor, the payments you recorded in the Payments card on their page.

So:

• A bill dated December and paid in January counts in January’s year.
• A bill you approved but never recorded a payment for counts for nothing.
• A payment made by card is left off the 1099-NEC, because the card company reports it. A payroll contractor’s card payment shows Card, not on the 1099-NEC.
• Money you paid the contractor outside Bokapsys’s bills or contractor payments (for example, a bank payment you only classified in your statements) is not counted. Record it as a bill payment or a contractor payment if you want it on the 1099.

Don’t record the same person both as a vendor and as a payroll contractor linked to that vendor; Bokapsys refuses a contractor payment for a contractor that is paid as a vendor, so nothing is counted twice.

Before you start

• You can see Tax → Filings. Your role must include the tax filing permissions; see Team and roles.
• A taxpayer is set up under Tax → Tax Setup → Taxpayers, with your full EIN and address. See Tax setup.
• Your IRS 1099 code (TCC) is saved on that taxpayer. The Transmitter Control Code is a five-character code the IRS gives you when you apply to use IRIS. The application takes time, so apply well before January.
• Each contractor has a completed Form W-9 from them. The W-9 is the IRS form a contractor fills in to give you their legal name, address and tax ID.
• Every payment to them for the year is recorded.

Step 1: Mark contractors and add their details

For a vendor:

1. Go to Invoicing (AP-AR) → Vendors and open the contractor.
2. Fill in the fields below from their W-9.
3. Tick Send this contractor a 1099.
4. Save. Repeat for every contractor.

Field on the vendor	What it means	Required for a 1099	Example	Where to find it
Legal name	The name the IRS knows them by. Used on the form instead of the display name when filled in	Strongly recommended	Jordan Lee Design LLC	W-9, line 1
Tax ID (EIN, SSN or ITIN)	Their taxpayer identification number. Type all 9 digits. It is stored encrypted, and afterwards only the last four digits are shown and the field reads Replace tax ID	Yes	12-3456789	W-9, Part I
Tax ID type	EIN (business), SSN (sole trader) or ITIN	Yes	EIN (business)	W-9, Part I: which box they filled
Address fields	Their mailing address, printed on the form	Yes	12 Oak St, Austin, TX 78701	W-9, lines 5 and 6
Send this contractor a 1099	Tells Bokapsys to include them	Yes	Ticked	Your decision: contractors and freelancers, not suppliers of goods

For a payroll contractor, enter the same details (name, Tax ID type, Tax ID, W-9 received and address, including the state) on their page under Payroll → People, and keep Gets a 1099-NEC at year end ticked. See Contractors.

Step 2: Create the 1099 forms

1. Go to Tax → Filings and open the 1099 Contractors tab.
2. Click Create 1099 forms (on the All Filings tab the same button is called 1099 batch). A window Generate 1099-NEC forms for contractors opens.
3. Check Tax year (it defaults to last year) and click Generate.
4. A window shows the result, for example 3 1099-NEC forms created for 2025 with Every form is ready to review. If anyone was left out, it names them: Left out because no tax ID is on file: …. Get their W-9, add the tax ID on the vendor page, then generate again. If nobody needs a form, it says so, for example that none of your contractors was paid $2,000 or more. Click Done.
5. The new forms appear on the 1099 Contractors tab, one row per contractor, with Box 1 (the amount paid), status Ready to review, due 31 January (or the next working day).
6. Click a row to check the form, and Download form to get the contractor’s PDF copy.

You can create the forms again for the same year whenever you fix a contractor’s details. It rebuilds each form that is still Ready to review. A form that is already signed or filed is left as it is, and the result window lists those contractors. To change a filed 1099, see Corrections.

Worked example

In 2026 you recorded these payments:

Who	Marked for a 1099	Paid in 2026	Tax ID	Result
Jordan Lee Design (vendor)	Yes	$8,400	On file	1099-NEC for $8,400 in Box 1 (nonemployee compensation)
Sam’s Web Fixes (vendor)	Yes	$1,500	On file	No 1099: below the $2,000 threshold
Office Supply Co (vendor)	No	$12,000	On file	No 1099: not marked
Pat Rivera (payroll contractor)	Yes	$3,000	Missing	Left out, named in the result window

Missing tax IDs

A 1099-NEC needs the contractor’s full nine-digit tax ID; the last four digits are not enough. Bokapsys never makes up a tax ID and never reports tax withheld that you did not actually withhold. A contractor with no full tax ID on file is left out and named, so you can get their W-9, add the number and create the forms again.

Step 3: Download the IRIS file and upload it

1. Go to Tax → Filings → All Filings and scroll to Send these to the government yourself.
2. Check Tax year.
3. In the 1099s for the IRS box, read “N forms”. A warning lists any contractor with no tax ID or no address on file. If your TCC is missing, the box says Add your IRS 1099 code under Tax Setup → Taxpayers before uploading.
4. Click Download 1099 file. IRIS takes up to 100 forms per submission, so with more than 100 forms the file is split and you see Download part 1, Download part 2 and so on. Download each.
5. Click Open IRS IRIS. This opens the IRS page about filing information returns with IRIS.
6. On the IRS site, sign in to IRIS with your TCC and upload each CSV file as its own submission. Keep the receipt IRIS gives you.
7. Send each contractor their own copy (the PDF from Download form on their filing).
8. In Bokapsys, open each 1099 filing, sign it, and record it as filed with Uploaded the 1099 file to the IRS and the IRIS receipt number. See Filing a return.

You can also download the file with Download 1099 file on any 1099-NEC filing page.

The file is a CSV in the exact column layout the IRIS upload accepts. Don’t add, remove or reorder columns.

How to check it worked

• Each contractor’s row shows the Box 1 amount you expect.
• The number in “N forms” matches the number of contractors you expected.
• After upload, IRIS shows your submission as accepted. Then the 1099 rows in Bokapsys show Filed.

Common problems

What you see	What it means	What to do
“No 1099-NECs have been generated for 2026 yet.”	The file is built from the generated forms	Click Create 1099 forms first
A contractor you expected isn’t there	They aren’t marked, were paid under $2,000, were paid by card, or the payments aren’t recorded in that year	Check the vendor’s tick box and their recorded payments
A contractor is listed under These contractors have no tax ID on file	Their full 9-digit tax ID isn’t on file	Add it from their W-9 and create the forms again
These contractors have no address on file	The contractor’s address is incomplete	Add it on their vendor or contractor page and create the forms again
“Add your full 9-digit EIN under Tax Setup → Taxpayers…”	Your own EIN is incomplete	Edit the taxpayer under Tax → Tax Setup → Taxpayers

Deadlines

The 1099-NEC is due 31 January to both the IRS and the contractor (moved to the next working day if it falls on a weekend or holiday). If you file 10 or more information returns of all kinds combined (W-2s, 1099s and 1095-Cs together) in a year, the IRS requires electronic filing; the filing page tells you where you stand. See Payroll filings.

To correct a 1099 that you have already filed, make the correction inside IRIS. See Corrections.

Related

VendorsWhere you mark contractors and add tax IDs.

BillsRecord the payments that 1099s count.

Filing a returnSign and mark a form as filed.

Contractors in payrollPaying contractors.