Matching Your eTIMS Invoices to Your Returns

Every month before you file, compare your eTIMS sales and purchase invoices with your books and your VAT return, and clear each difference. Then, once a year, do the same for your income tax return, adding withholding tax certificates and customs records. KRA already runs this comparison, so you want to find the gap first.

What KRA is already checking

• VAT: KRA pre-fills the VAT return from invoices sent through eTIMS, updated daily. It is still your return, and you must check it.
• Income tax: in a public notice, KRA said it would validate income and expenses from 1 January 2026, starting with 2025 returns. It checks them against eTIMS records, gross withholding tax and customs import records.
• Pre-filled returns: since 1 July 2026, section 75 of the Tax Procedures Act lets KRA generate a return for you. It must issue it by the end of January, and you have two months to confirm or amend it.
• Expenses: section 16(1)(c) of the Income Tax Act bars a deduction where the invoice did not come through eTIMS, unless the transaction is exempt. Section 23A(4) of the Tax Procedures Act lists items that may be left out, including salaries, imports, interest and airline tickets. Our expenses guide covers this in more detail.

The monthly check

Do this a few days before the 20th, using the latest version of the return.

1. Sales. Export your eTIMS sales and match them to your sales ledger, by invoice date. KRA places sales in the tax period of the invoice date, not the date of transmission.
2. Sales not yet on eTIMS. Declare all sales for the period, whether or not they were transmitted. KRA’s guidance says you can increase pre-filled sales, but you cannot reduce them.
3. Purchases. Compare your supplier invoices with the pre-filled purchases. Only valid, transmitted invoices carrying your PIN can be claimed.
4. Items that should not be claimed. Remove any purchase that is not yours or whose input VAT is not allowed. The return will not split input VAT between taxable and exempt sales for you, so do that yourself.
5. Imports. Check that customs entries show as settled or removed. KRA only allows a claim once they do.
6. Sign off. Keep a one-page note showing eTIMS total, books total and return total, with each difference explained. This is the paper you will want in an audit, and it is part of the records you must keep.

Common gaps and how to fix them

What you see	Likely cause	What to do
eTIMS sales are higher than your books	Sales not recorded, or a duplicated invoice	Record the sale, or raise a credit note if the invoice is wrong
Your books are higher than eTIMS	Invoices not issued or not transmitted	Issue them, check the device connection and declare the sale
Wrong or missing buyer PIN	Captured wrongly at invoicing	Seller issues a credit note and reissues the invoice. The buyer claims it the next month
Purchase missing from the return	Supplier has not transmitted the invoice	Ask the supplier to transmit it, and claim it in a later period
Sale wrongly shown as zero-rated or exempt	Device set up wrongly	Have your device supplier correct it
Message that a PIN is not eligible for input deduction	Supplier is on KRA’s VAT Special Table	You cannot claim from that supplier until it is removed

Two time limits to watch

• Input VAT. Section 17(2) of the VAT Act allows the claim within six months after the end of the tax period of the purchase. KRA’s FAQ counts six months from the invoice date, which can be slightly shorter, so work to the earlier date. More detail is in our input VAT guide.
• Credit notes. Under section 16 of the VAT Act, a credit note may only be issued within six months of the original invoice.

The yearly check

Before filing income tax, tie these together:

• Income: total eTIMS sales, plus any income from withholding tax certificates, against the income in your return. A client’s withholding certificate that exceeds your declared income is an obvious flag.
• Expenses: eTIMS purchases and customs entries, against your expense lines. Note anything claimed without eTIMS and why it is exempt.
• Timing: explain differences, such as sales invoiced in December but recorded in January.

KRA’s notice says you can ask your account manager for your eTIMS schedules of annual income and expenses. If you receive a pre-filled return, check it against your own books within the two months, rather than confirming it on trust.

What happens if you do nothing

Under section 86 of the Tax Procedures Act, as replaced by the Finance Act 2026, failing to issue an electronic invoice can cost the higher of 5 percent of the tax due, or a minimum of KES 100,000 for a company or KES 10,000 for an individual. KRA must first ask for your reasons. A mismatch can also lead to an assessment, which you have 30 days to object to.

If this check is taking too long each month, our accounting team can run it with your monthly close.