Reconciling client withholding certificates

How a firm matches a Kenyan client's withholding tax certificates to its income before filing, now that KRA checks returns against withholding data.

By Achekam · 11 October 2026 · 4 min read · For Accountants & audit firms in Kenya

A consulting client invoices a dozen corporate customers, and most of them withhold tax from its fees. By year-end the client holds a pile of withholding certificates, some for invoices it remembers, some it cannot place, and probably a few it never received. The annual return claims those certificates as credits, and the income behind each of them has to be in the return too.

That match used to be something KRA might test later. It is now something KRA tests on submission. A firm that reconciles certificates against income before filing avoids two problems at once: credits the client cannot support, and income KRA can see that the client forgot to declare.

Why the match matters now

KRA says that from 1 January 2026 it validates the income and expenses declared in individual and non-individual income tax returns against TIMS/eTIMS data, withholding income tax data and customs import records. The validation applies when returns for the 2025 year of income or accounting period are submitted.

Withholding data is the most direct of those comparisons. Every certificate tells KRA that a customer paid the client a gross amount and withheld tax from it. If the client's declared income is lower than the gross amounts on its certificates, the gap is visible to KRA without anyone asking for documents.

How certificates reach the client

KRA says that once the payer remits the tax, a withholding tax certificate generated on iTax is sent automatically to the payee, and the payee claims it when filing its annual return. The certificate exists only after the payer has remitted; a customer that withheld but did not pay over the tax has produced no certificate.

KRA also explains when withholding settles the matter and when it does not. For payments to non-residents with no permanent establishment in Kenya, withholding tax is a final tax. For most payments to residents it is not final: the payee must declare the income and the withholding certificates in its annual return and pay any balance. A resident client's certificates are therefore credits against its own tax, not the end of the story. The rates for fees are in withholding tax on professional fees.

Matching certificates to invoices and receipts

Ask the client for every certificate iTax has sent it for the year, and set them against its sales records:

1. List each certificate with payer, date, gross amount and tax withheld.
2. Match each to the invoice or invoices it relates to, and to the receipt in the bank statement.
3. Confirm that the gross amount on the certificate is included in the income the return declares.
4. List invoices to customers who should have withheld but for which no certificate has arrived.
5. List certificates that match no invoice, or that show a gross amount different from the invoice.
6. Total the certificates to be claimed and compare the total with the credit in the draft return.

The bank statement is the useful middle column. A customer that paid net of withholding shows a receipt below the invoice; that difference should equal the tax on a certificate.

Missing and wrong certificates

Missing certificates are the common problem. Where a receipt shows tax withheld but no certificate exists, the customer may not have remitted the tax yet, or may have quoted a wrong PIN when it did. The client should ask the customer for the remittance details and the certificate. Until one exists, do not claim the credit.

Wrong certificates need the same care. A certificate with the wrong gross amount or the wrong PIN overstates or misdirects a credit, and because the payer generated it, the correction starts with the payer.

The iTax portal offers public checkers to verify a PIN, a tax compliance or exemption certificate or excise licence, a withholding certificate, a withholding agent, a control unit serial number and a control unit invoice number. Use the withholding certificate checker on the iTax portal for any certificate the client did not receive through its own iTax account, such as a copy forwarded by a customer, before the credit goes into the return.

Documenting the work in Achekam's return workflow

Staff can open a Kenyan tax profile for the client and start a return that moves through prepare, review and approve by different people. Once approved, the return's rule snapshot and figures are frozen, and an amendment is a new version rather than an overwrite. The reconciliation belongs with the preparer's work on that return, so the reviewer tests it and the approver sees it before the figures are frozen.

Where the client sends its ledger rather than a sales listing, a firm can upload a general ledger in the layout the client's accounting package exports. Achekam adds it up into a trial balance and checks every printed account total against its own sum, naming any difference rather than quietly fixing it. A sales ledger that agrees with its own totals is a sound base to reconcile certificates against.

The client letter on gaps

End with a letter, not just a working paper. The client has to act on the gaps, and some of them can only be fixed by its customers.

This reconciliation is one of the core schedules in preparing a client's IT2C company return, alongside the eTIMS checks in checking a client's eTIMS schedules.

General guidance only, not advice on your own circumstances. Tax and payroll rules change: check the current position with the authority or your adviser.