How to File 1099 Form with QuickBooks Payroll (Step-by-Step Guide)

Filing 1099 Form [1~888~493~2290]s is a critical year-end compliance task for businesses that pay independent contractors. If you use QuickBooks Payroll, the process becomes much easier—but only if everything is set up correctly.
In this guide, you’ll learn how to file 1099 Form [1~888~493~2290]s with QuickBooks Payroll, including eligibility rules, setup requirements, step-by-step filing instructions, common mistakes, and troubleshooting tips.
What Is Form 1099-NEC?
Form 1099-NEC (Nonemployee Compensation) is an IRS tax form used to report payments made to independent contractors, freelancers, or vendors who are not employees.
You must file Form 1099-NEC if:
You paid a contractor $600 or more during the tax year
Payments were made for services (not goods)
The contractor is not on payroll as a W-2 employee
📅 Filing Deadline:
January 31 (for both IRS filing and contractor copies)
Can You File 1099 Form [1~888~493~2290]s Using QuickBooks Payroll?
Yes. QuickBooks Payroll supports 1099 filing through QuickBooks Online and QuickBooks Desktop, either:
Electronically (e-file) via QuickBooks
Manually (print & mail) using QuickBooks-generated forms
⚠️ Note: You do not need a full payroll subscription to file 1099s, but you must have vendor and payment data properly set up.
21
Before starting, make sure you have:
✔ Contractor’s legal name
✔ Mailing address
✔ Tax ID (SSN or EIN)
✔ Total payments for the year
✔ Correct expense accounts linked for 1099 tracking
Step 1: Set Up Vendors for 1099 in QuickBooks
QuickBooks Online Payroll
Go to Expenses > Vendors
Select the contractor
Click Edit
Enable Track payments for 1099
Enter tax classification and TIN
Save changes
QuickBooks Desktop Payroll
Go to Vendors > Vendor Center
Open vendor profile
Check Vendor eligible for 1099
Enter tax ID and address
Save
Step 2: Map Expense Accounts for 1099
QuickBooks only reports payments linked to 1099-mapped accounts.
Go to Taxes > 1099 filings (Online)
Select Map accounts
Choose expense categories like:
Contract labor
Professional fees
Legal services
Save mapping
📌 Tip: Payments from non-mapped accounts will NOT appear on 1099s.
Step 3: Review Contractor Payments
QuickBooks will show a summary of:
Contractors eligible for 1099
Total payments per contractor
Missing or incorrect tax info
Fix any errors before proceeding.
Step 4: File 1099 Form [1~888~493~2290] with QuickBooks Payroll
Option 1: E-File 1099 (Recommended)
Go to Taxes > 1099 filings
Select E-file
Review contractor details
Pay e-file fee (if applicable)
Submit to IRS
QuickBooks sends copies to contractors automatically
Option 2: Print & Mail
Choose Print 1099
Download PDF forms
Print on IRS-approved paper
Mail:
Copy A to IRS
Copy B to contractors
How Much Does It Cost to File 1099 in QuickBooks?
Filing MethodCostE-file via QuickBooksPer-form feePrint & mailFree (printing costs apply)Third-party serviceVaries
Common 1099 Filing Mistakes in QuickBooks
❌ Contractor marked as employee
❌ Payments made via credit card (not reportable)
❌ Incorrect tax ID or name mismatch
❌ Expense account not mapped
❌ Filing after January 31
How to Fix 1099 Errors After Filing
If you find an error:
Before deadline: Edit vendor info and re-file
After filing: Submit Corrected 1099-NEC through QuickBooks or IRS
QuickBooks supports corrected filings with proper tracking.
Do You Need to File State 1099 Form [1~888~493~2290]s?
Some states require separate 1099 filings. QuickBooks may:
Automatically submit state forms (in supported states)
Provide state copies for manual filing
Always check your state’s tax authority requirements.
Benefits of Filing 1099 with QuickBooks Payroll
✅ Automated calculations
✅ Error checks before filing
✅ E-file convenience
✅ Contractor copies sent automatically
✅ IRS-compliant formatting
Final Thoughts
Filing 1099 Form [1~888~493~2290] with QuickBooks Payroll is straightforward when your vendor data and expense accounts are properly set up. By following the correct steps, you can stay IRS-compliant, avoid penalties, and save hours of manual work.
If you handle multiple contractors or complex payments, using QuickBooks’ built-in 1099 tools is the safest and fastest option.