You filed your returns, paid your dues via M-Pesa, and even got that confirmation message. Months later, you log into iTax and boom—a shocking balance stares back at you. Panic mode? Don’t. You’re not alone. This frustrating glitch hits thousands of Kenyans every filing season. It’s usually a system lag or a simple mismatch, not a new tax bill.
This article breaks down exactly why iTax is showing you owe taxes you already paid and gives you a direct, action-focused guide to clear your name (and your portal). We’ll cover the common errors, the documents you need from your phone or laptop, and the exact steps to take, whether you’re in Nairobi, Mombasa, or upcountry.
Common Reasons Your iTax Shows a False Debt
Before you stress, understand the culprit. The Kenya Revenue Authority (KRA) system isn’t perfect. Here are the usual suspects behind that phantom debt.
1. The Dreaded Payment Processing Lag
This is the number one reason. You paid via M-Pesa, bank, or agent, but the payment hasn’t been “matched” to your specific tax obligation in the iTax system. It’s like dropping a letter in a post box in Hurlingham—it’s sent, but delivery takes time. During peak periods like the June 30th deadline rush, this lag can stretch to weeks.
The system sees an unpaid obligation and a floating, unmatched payment. Until a KRA officer manually or systemically links them, your statement will show arrears.
2. Incorrect Payment Reference Number
You must use the exact, unique Payment Registration Number (PRN) generated on iTax for each obligation. If you used an old PRN, typed one digit wrong, or used a generic paybill number without a PRN, the payment floats in cyberspace.
It’s like sending school fees to the wrong bank account. The money is gone from your pocket, but it never reached its intended destination in the KRA’s books.
3. Filing Returns Without Payment
Filing your return and making payment are two separate steps on iTax. You can file (declare what you owe) and close the browser, thinking you’re done. But if you didn’t complete the payment step, you have a declared debt. Always check for a payment confirmation from KRA, not just your bank.
4. Interest and Penalties Accrual
If your initial payment was even one day late, KRA’s system auto-calculates penalties and interest. You might have paid the principal tax but not these additional charges. The system will keep showing a balance for the penalties, which continue to grow daily.
Step-by-Step: How to Resolve the iTax “Ghost Debt”
Time to take action. Follow these steps in order. Have your KRA PIN, phone, and laptop ready.
Step 1: Gather Your Evidence (Don’t Skip This)
You can’t argue with KRA without proof. Download or screenshot these:
- M-Pesa Statement: Go to your M-Pesa menu > Lipa na M-Pesa > My Transactions. Find the KRA payment. Screenshot the whole thing showing date, amount, and transaction code.
- Bank Slip or Statement: If you paid via bank, get the bank slip or a PDF statement entry showing the payment to KRA.
- iTax Payment Receipt: Log into iTax, go to “Payments” > “View Receipts.” Download the receipt for the disputed payment if it appears there.
Save these on your phone. You’ll need them for the next steps.
Step 2: Initiate Payment Matching on iTax
Sometimes you can fix this yourself. Log into iTax and navigate to “Payments” > “Payment Registration” > “Match Payment.”
Here, you can try to manually attach a floating payment to the correct tax head. Enter the transaction details from your M-Pesa or bank slip. If successful, your balance should clear within 24-48 hours. If the option is greyed out or fails, move to Step 3.
Step 3: The KRA Helpdesk & Raia Center Visit
If self-help fails, you need human intervention. First, call the KRA helpline +254 020 4 999 999 or 0711 099 999. Be patient; lines are busy. Have your PIN and evidence ready.
If the call doesn’t resolve it, a physical visit is your strongest move. Go to your nearest KRA Tax Service Office or Huduma Centre. The ones at Times Tower (Nairobi), Mombasa’s Nkrumah Road, or Kisumu’s Mega Plaza are well-equipped for this.
The Kenyan-Specific Guide: Navigating KRA Like a Pro
Dealing with government systems in Kenya requires a specific strategy. Here’s the local knowledge you need.
Timing is Everything: Avoid the Rush
Never visit a Huduma Centre or KRA office at month-end or during the mad rush before a deadline (like late June). You’ll waste a whole day in queues. Go mid-week, mid-month, and be there by 7:30 AM. You’ll be done by lunchtime, unlike showing up at 10 AM and leaving at 5 PM.
Consider the weather too. Going during the long rains (March-May) means chaotic traffic in Nairobi. Leave extra early or plan your visit for a drier season to avoid the stress.
What to Carry & Say at the Huduma Centre
Walk in prepared. Have your:
- Original National ID and a copy.
- KRA PIN certificate.
- Printed copies of your payment evidence (M-Pesa screenshot, bank slip).
- A written summary: “My PIN is A001234567X. I paid KSH 5,400 on 15/04/2024 via M-Pesa transaction code RBX4F5 for January 2024 Rental Income. iTax still shows arrears.” This helps the officer quickly.
Be polite but firm. Ask for a “payment reconciliation” for your account. If the officer says “wait for 72 hours,” politely ask for a reference number for your enquiry.
Costs and Realistic Expectations
Fixing this shouldn’t cost you money, only time and maybe transport. A boda boda trip to the centre might be KSH 200-500. If you’re told to pay “penalties” you dispute, don’t pay on the spot. Ask for a detailed calculation. If the error was KRA’s, they should waive it.
Remember, if the unresolved debt is on your certificate of good conduct or CRB listing, it gets serious. This is why acting fast is key, not waiting for “the system to update.”
How to Prevent This iTax Headache Next Time
Once resolved, follow these rules to avoid a repeat drama.
Double-Check the PRN Every Single Time
When generating a PRN on iTax, treat it like a password. Copy-paste it if possible. When paying via M-Pesa, verify the PRN on the confirmation screen matches exactly. One wrong digit and you’re back in this mess.
File AND Pay in One Sitting
Don’t file your return and plan to pay “later today.” Life happens. Complete the entire process—generate PRN, make payment, get confirmation—in one uninterrupted session on your phone or computer.
Download and Save Official Receipts
Immediately after payment, go to iTax > Payments > View Receipts. Download the PDF receipt and save it in a dedicated folder on your phone or email. This is your golden ticket if issues arise later. Don’t rely on M-Pesa messages alone.
When to Seek Professional Help
Most cases can be solved by you. But if the amount is large (e.g., KSH 500,000+), involves complex issues like VAT or corporate tax, or if KRA is uncooperative, hire a licensed tax agent.
Ask for referrals from other business owners. A good agent in Nairobi might charge from KSH 5,000 to resolve such a mismatch, but they know the internal processes and can get it done faster. It’s worth it for peace of mind and to protect your business from penalties.
Seeing a tax balance you already settled is frustrating, but it’s usually a fixable system error. The key is acting quickly with the right evidence. Don’t ignore it, as penalties can grow. Gather your M-Pesa or bank proof, attempt online matching, and if stuck, make that early morning trip to Huduma Centre. Protect yourself next time by being meticulous with PRNs and saving receipts. Your iTax portal should reflect your compliance, not cause unnecessary panic.
Got a different iTax issue you’re battling? Share your experience in the comments below—your tip might help another Kenyan solve their problem faster.