Mississippi Form 89-140 Annual Information Return: What QuickBooks Users Need to Know

Each year, QuickBooks users who run payroll or issue 1099s in Mississippi must submit Form 89-140, the state’s Annual Information Return. This is not a payment form — it is a transmittal cover sheet that accompanies the state copies of W-2s, 1099s, W-2Cs, and 1099-Rs. Confusion often arises about the correct deadline, the requirement to file separate forms for each category, and what to do when the tax withheld doesn’t match the amounts already remitted. Here is a plain-language breakdown of how this form works inside QuickBooks Desktop and Online.

Who Must File

Any employer that withholds Mississippi state income tax from wages, or that is required to withhold it, must file Form 89-140 for each information-return category. That means one 89‑140 for the batch of W-2s, another for 1099s, another for 1099-Rs, and yet another for W-2Cs if corrections were issued. QuickBooks cannot combine categories; you must complete and submit a separate transmittal for each.

Filing Deadlines

• W-2 returns, paper or e-file: due January 31. If you are filing ten or more W-2s, electronic submission is mandatory.
• 1099s and other information returns (1099-R, etc.): due February 28, both for e-file and paper filers.

If you file after January 31 — even by a day — you lose the option to submit on paper for W-2s; the state requires electronic upload of the file instead.

Mailing Address (Paper Filers)

When mailing the completed Form 89-140 along with the attached W-2s or 1099 copies, send them to:

Department of Revenue Withholding Tax Division PO BOX 23058 Jackson, MS 39225-3058

Do not include a payment with this form. Payments must be made separately on the appropriate periodic Form 89-105 (monthly or quarterly). Sending a check with the 89-140 will not credit your account.

How QuickBooks Handles the Form

Inside QuickBooks, when you generate state payroll reports, many of the fields on Form 89-140 are pre-filled from your company, payroll, and employee data. In most cases, if all payroll information was entered correctly during the year, you will only need to review a few blank fields and supply missing numbers.

For the W-2 category, QuickBooks prefills the number of forms, total wages, and tax withheld. For 1099s and 1099-Rs, you must complete a 1099 worksheet within QuickBooks; the program then populates the lines (A through D) that flow into the form. For W-2C correction forms, you will need to enter the corrected counts and amounts manually.

Always double-check the figures that QuickBooks didn’t fill in — particularly if you had mid-year employee additions, terminations, or out-of-state allocations.

Out‑of‑Balance Accounts

A common frustration is a mismatch between what was withheld and what was remitted. Here is how the state expects you to handle it:

• Underpayment (tax withheld > tax remitted): Do not attempt to pay the shortage with the 89-140. Instead, file an additional Form 89-105 for the month or quarter that covers the shortfall, and send the payment separately.
• Overpayment (tax withheld < tax remitted): Determine which period produced the overpayment and file an amended Form 89-105 for that period. Do not reduce the amounts on the 89-140.

QuickBooks can help spot these discrepancies if you run a payroll liability reconciliation report before generating the annual return.

Electronic Filing Option

If you prefer or are required to file electronically, Mississippi offers a secure portal for uploading the state copy of your W-2s and 1099s. When you use the electronic submission, you do not need to mail a paper Form 89-140. This method is mandatory if you are filing ten or more returns in any one category, or if you are past the January 31 deadline for W-2s.

Final Reminder

Keep a separate Form 89-140 for each type of information return. Mixing W-2s and 1099s on the same transmittal will cause processing delays and may generate a penalty notice. If you ever need to correct a previously filed return, use the same category’s form with corrected figures.

For more general QuickBooks payroll guidance, visit QuickBooksUsers.com.