Disclaimer: This information is provided for general reference only. Always verify filing and reporting details with your CPA or tax advisor before submitting forms. Cyncly does not provide tax or legal advice.
This guide explains how to generate, review, and print 1099 and 1096 forms in RFMS for year-end reporting.
It also includes optional steps for handling 1099 data create through Accounts Payable (AP) and transferring it into Human Resources (HR) so that all 1099s can be processed in one run.
Use this article after you have completed year-end reconciliation and run your first payroll of the new year and are ready to generate, review, and print 1099s and 1096s for U.S. recipients.
If you also issue W-2s, see Processing W-2s in RFMS.
If you process 1099s for suppliers through the Accounts Payable module rather than through Human Resources, see Processing Accounts Payable 1099s in RFMS for that workflow.
| Step | Action Items |
|---|---|
| 1. Confirm Readiness |
☐ Verify you're on the latest RFMS version. ☐ Confirm the HR Update is installed and displays the current tax year. ☐ Back up company data before starting. |
| 2. Generate 1099 Information (HR) |
☐ Go to Accounting > File > Human Resources > File > End of Year > Generate W-2 and 1099 ☐ Confirm the correct Tax Year appears at the top of the screen. ☐ Verify state and locality ID numbers for every reporting jurisdiction. ☐ Mark “Post on 1099s” for each state that requires separate reporting. ☐ (Optional) Add locality codes if applicable. ☐ Review deduction batches (e.g., retirement, insurance, or benefit deductions) that might affect 1099 totals. ☐ (Optional) Select Exclude Voids to omit voided checks from the data set. ☐ (Optional) Enter a Minimum Gross Amount to exclude suppliers below the reporting threshold. ☐ Click Process to generate 1099 records. ☐ Once complete, review the generated information under Browse W-2/1099 Information before continuing. Tip: The Post on 1099s and Has Tax ID fields help control which suppliers are included in 1099 generation. |
| 3. Review and Edit 1099 Records (HR) |
☐ Go to File > End of Year > Browse W-2 and 1099 Information. ☐ Use the drop-down to select Contractor or 1099 Earnings. ☐ Review each contractor record carefully. ☐ Use Edit to correct data or Delete to remove an entry from the batch. ☐ Confirm that Box 1 (Non-Employee Compensation) and any other applicable boxes match Accounts Payable totals. ☐ Check that supplier names, addresses, and TINs are accurate and formatted properly. ☐ Save all updates before continuing. Note: Manual edits here update only the form data—they do not modify payroll or AP history. Always verify corrections with accounting staff before final submission. |
| 4. Generate 1099s from Accounts Payable (AP) |
☐ Review supplier records: verify name, address, and tax ID. Confirm proper Taxpayer Identification Number format. See note below. ☐ Check Do Not Print Tax Document for vendors who shouldn’t receive a 1099. ☐ Go to File > End of Year > Generate AP 1099 Information. ☐ (Optional) Run once with Has Tax ID unchecked to audit missing IDs. ☐ Review the AP 1099 Edit Listing report to confirm which suppliers require forms. ☐ Regenerate with Has Tax ID checked when ready. Note: For a full walkthrough of this process please see the article Processing Accounts Payable 1099s in RFMS. |
| 5. Transfer AP 1099s to HR (if applicable) |
☐ Go to File > End of Year > Transfer AP 1099 Information. ☐ Enter your state abbreviation and state tax ID. ☐ Click OK to move AP 1099s into HR. ☐ Verify all 1099s now appear in Browse W-2 and 1099 Information. |
| 6. Generate Reports |
☐ Go to Human Resources > Reports > End of Year > Reports. ☐ Run and save: Detail Report |
| 7. Print or Save 1099/1096 Forms |
☐ Go to Reports > End of Year > W-2 and 1099 Forms. ☐ Select the 1099/1096 tab. ☐ Confirm business name, EIN, and contact details. ☐ Choose which form to create (1099 NEC, 1099 MISC, or 1096). ☐ Choose print order (Name or SSN). ☐ Set output directory and click Generate to create PDFs. ☐ Print on plain paper first, then on official pre-printed forms. ☐ Adjust PDF scaling if alignment is off. Note: Once A/P 1099 data is transferred to HR, all supplier and contractor forms can be printed or e-filed together. For more information see Printing Year-End Tax Forms. |
| 8. Optional: Export or Import Data |
☐ Export to CSV ☐ Go to Reports > End of Year > Export Tax Forms. ☐ Select 1099 MISC or 1099 NEC, choose location, and click Process. ☐ Share the CSV securely with your accountant if they print or file. ☐ Import from CSV ☐ Go to Reports > End of Year > Import Tax Forms from CSV. ☐ Click Create Empty File to download the template. ☐ Fill in data and re-import using Process. |
Verify TIN Format Before Generating 1099 Files
The Taxpayer Identification Number (TIN) Type that appears in your 1099 file depends on how the number is entered in the supplier record.
Format Entered in RFMS |
Example | TIN Type in File |
|---|---|---|
| Employer Identification Number (EIN) | 12-3456789 |
1 |
| Social Security Number (SSN) | 123-45-6789 |
2 |
| Any other format | — | Blank (invalid) |
Tip: Always confirm that supplier Tax ID numbers use the correct format before generating the 1099 file. Incorrect formats can cause missing TIN Type values and prevent successful e-filing.
Exclude Suppliers That Don't Require 1099s
If suppliers are included by mistake, go to Accounting > File > Human Resources > File > End of Year > Browse A/P 1099 to delete unneeded records.
You can also add or edit supplier records from this same screen before transferring them to Human Resources.
Converting 1099 NEC to MISC
If a supplier’s 1099 form type should be MISC instead of NEC, see Converting a 1099-NEC to a 1099-MISC for instructions.
Importing Tax Data from a CSV File
If you’re importing W-2 or 1099 data from an external source, you can generate a blank Tax Form Import (.csv) template from Human Resources > Reports > Import Tax CSV. Enter the required data and import the completed file to add or update form information.
Note: Selecting Add Duplicate Tax Form numeric totals to existing matching Tax Form during import will add the imported amounts to any existing totals for that employee or subcontractor, rather than replacing them.
Imported forms can be reviewed or edited from Accounting > Human Resources > File > End of Year > Browse W-2 & 1099 Information.
E-Filing Reminder
If you file 10 or more total information returns (W-2s + 1099s), you must e-file. See Electronic Filing W-2s and 1099s in RFMS. To e-file 1099s, set up an IRS IRIS (Information Returns Intake System) account in advance.
Quick Troubleshooting
| Issue | Resolution |
|---|---|
| Tax year incorrect | Install the latest HR Update |
| Supplier missing tax ID | Edit supplier file and re-run AP 1099 Edit Listing |
| Misaligned print | Adjust PDF scaling or printer driver |
| AP 1099s missing from HR | Re-run “Transfer AP 1099 Information” |
| Manual edits not reflected in reports | Confirm with accountant for adjusting entries |
Next Steps
To e-file 1099s, see:
To print final forms, see:
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