How to Reconcile eTIMS Invoices With Your Accounting Records in Kenya

To reconcile eTIMS invoices with your accounting records, match every invoice transmitted to the Kenya Revenue Authority (KRA) with the corresponding sales, purchase or credit note entry in your books. Compare the invoice number, date, supplier or customer PIN, taxable value and VAT amount, then correct any discrepancies before filing your returns.

This eTIMS reconciliation is important because KRA uses eTIMS data to pre-fill VAT returns. From 1 January 2026, it also uses the data to validate income and expenses in income tax returns. Buyer-Initiated Invoices (BII), which buyers must raise on behalf of small suppliers with annual turnover of KES 5 million or less, appear under your PIN. They need the same checks and must also match your purchase records.

Why do eTIMS records and your books differ?

eTIMS holds what was transmitted to KRA, while your books hold what your team recorded. The eTIMS vs books gap usually comes from one of four sources:

• Untransmitted invoices: An invoice saved in your system never reaches eTIMS because of a network outage or an eTIMS invoice failure that nobody followed up on.
• Manual entries: A sale or purchase is posted straight to the ledger without an eTIMS invoice, or for a different amount from the eTIMS invoice.
• Timing differences: An invoice dated 30 September is posted in October. KRA pre-fills returns by invoice date, so the posting period matters.
• Credit notes: A credit note exists on one side only or is linked to the wrong original invoice.

What data should you compare?

Check these five details for every invoice. Matching totals alone may hide errors, because two discrepancies can offset each other.

• Invoice number (your internal number and the eTIMS number returned by KRA)
• Invoice date, which decides the tax period
• Customer or supplier PIN
• Taxable amount before VAT
• VAT amount and the rate applied (16%, 8%, 0%, exempt or non-VAT)

Use reports covering the same date range. Match invoices individually before comparing the totals.

How do you reconcile sales invoices?

An eTIMS sales reconciliation compares the invoices you transmitted with the sales register in your books. Follow these steps each month:

1. Export the eTIMS sales listing for the month.
2. Export the sales register from your books for the same dates.
3. Match each eTIMS invoice to its book entry by invoice number.
4. Compare date, customer PIN, taxable value and VAT on every matched pair.
5. Mark every invoice that appears on one side only as an exception.
6. Record the reason and corrective action for each exception.
7. Have a reviewer sign off on the adjusted totals.

Sales invoice reconciliation sample

The sample below shows a September sales reconciliation in Kenyan Shillings (KES):

Note: The figures assume both reports use the same basis, either taxable values or VAT-inclusive invoice values. Do not mix the two. 

How do you reconcile purchase invoices?

Purchase reconciliation helps ensure that your accounting records agree with the supplier invoices available in eTIMS. It also helps identify invoices that may not qualify for input VAT claims or allowable expenses.

To reconcile eTIMS invoices for purchases, follow these steps each month to identify discrepancies and verify input VAT claims:

1. Download the purchase invoices transmitted under your PIN for the month.
2. Export the purchase register from your accounting system for the same period.
3. Match each invoice using the supplier PIN and invoice number. Also compare the invoice date and taxable value to identify duplicate entries or differences in the recorded amounts.
4. Compare the VAT amount on each matched invoice with the input VAT recorded in your books. Check that the purchase qualifies for an input VAT claim before including it in your return.
5. Check the approval status of BII raised for eligible purchases from non-VAT-registered suppliers. The seller has 30 days to approve or reject an invoice raised through eCitizen or the *222# USSD service. If the seller does not respond, the request is rejected automatically. Follow up on pending requests and exclude rejected invoices from your valid purchase records until resolved.
6. Contact suppliers to resolve discrepancies. Request transmission of missing invoices, correction of incorrect PIN details or resolution of failed transmissions. Track late-transmitted invoices separately and check the applicable six-month input VAT claim deadline.
7. Update your accounting records after verifying each correction. Retain the relevant invoices, credit notes and supporting documents, then reconcile the final purchase and input VAT totals with the available eTIMS data before filing.

Purchase reconciliation sample

The sample below shows a September purchase reconciliation in KES:

How should you handle credit notes and corrections?

A transmitted eTIMS invoice is corrected through a credit note that refers to the original invoice. Match each eTIMS credit note to its source invoice before matching it to the books, and check these points:

• The credit note quotes the correct original invoice number.
• The PIN matches the original invoice.
• The credit amount does not exceed the original invoice value.
• The VAT reversed uses the original rate.
• The credit note falls in the same period in eTIMS and in the books.

Where a correction needs a new invoice, issue the credit note first and then a fresh invoice. A credit note recorded only in the books creates an eTIMS mismatch. It lowers ledger sales but not the pre-filled VAT return, and pre-filled sales cannot be reduced at filing. BII sellers can also raise credit notes against the original invoice, including through USSD.

What are the common eTIMS mismatch cases and how do you fix them?

Most mismatches follow a few patterns. The table below lists the usual cause and fix for each:

How often should you reconcile?

A regular invoice reconciliation routine in Kenya helps identify discrepancies early and reduces the workload at month-end. The table below shows how to spread the checks across the month: 

How does accounting software simplify eTIMS reconciliation?

Integrated accounting software reduces manual work during eTIMS reconciliation. When your system is integrated with eTIMS, invoices are transmitted directly from saved vouchers, and the eTIMS invoice number returned by KRA is recorded against the corresponding voucher. You can then use two reports to identify and resolve discrepancies:

• Matching report: Shows each voucher's eTIMS transmission status, invoice number and transmitted values.
• Exception report: Lists vouchers that failed transmission, were not transmitted or were modified after transmission.

However, software cannot resolve every discrepancy. You must still follow up with suppliers on missing invoices and pending BII approvals. When evaluating accounting software in Kenya, check whether it does the following:

• Tracks eTIMS status at voucher level
• Links credit notes to their original invoices.

A reconciled month confirms that every expense you plan to deduct has a valid eTIMS invoice behind it and that the revenue in your financial reports matches the sales KRA already holds. Start with the current month, clear exceptions in order of their tax effect and chase non-compliant supplier invoices early, since each one is a deduction at risk.

Fewer exceptions arise when invoices are recorded and transmitted from one system. With TallyPrime, you can generate eTIMS invoices and credit notes from the same vouchers you record in your books, so less needs matching at month-end.

FAQs

1. How do I reconcile eTIMS invoices with my books?

Export the eTIMS invoice data and the matching register from your books for the same period. Match each invoice on number, date, PIN, amount and VAT, then correct every item found on one side only.

2. Why does my eTIMS sales total differ from my books?

The usual causes are failed transmissions, sales posted without an eTIMS invoice, entries posted in a different month from the invoice date, and one-sided credit notes. Check the date range of both reports first.

3. How often should eTIMS reconciliation be done?

Complete a full eTIMS reconciliation every month before you prepare the VAT return. Add daily transmission checks and a weekly sales match to catch an eTIMS mismatch early.

4. Where can I download my eTIMS invoice data?

Sales invoices issued through the eTIMS taxpayer portal can be exported from the portal’s reports. Purchase invoices transmitted with your PIN appear in the pre-filled purchase details of the VAT return on iTax.

5. What should I do with invoices recorded in my books but not in eTIMS?

First confirm that the transaction is genuine and correctly dated. For a sale, generate or retransmit the eTIMS invoice. For a purchase, ask the supplier for a compliant invoice with your PIN, because input VAT cannot be claimed on a manual invoice.

6. Can accounting software reconcile eTIMS invoices automatically?

Software integrated with eTIMS can match sales and credit notes to their transmitted records and list the exceptions. Supplier-side gaps, such as a missing PIN or an unapproved BII invoice, still need manual follow-up.