Practical guide – Kenya VAT & eTIMS
How to reconcile VAT, eTIMS and iTax in Kenya
Kenyan VAT-registered businesses need to check that the sales and purchases in their books agree with eTIMS invoice records and with the VAT figures that appear in iTax. KRA pre-fills the auto-populated VAT return with tax information from iTax, TIMS, eTIMS and customs systems, and it requires taxpayers to verify and confirm those figures before filing. This guide explains a practical monthly review. It is not tax advice. It does not claim that VisionONE is a KRA-approved eTIMS integrator, and it does not claim that VisionONE files returns on iTax.
Sources checked: 12 November 2026.
Why this reconciliation matters
If an invoice is in your ledger but not in eTIMS, or in eTIMS but not in your ledger, the auto-populated return and your books will differ. A monthly reconciliation gives your finance team a chance to investigate differences before the return is filed. Official reference: KRA’s guidance on the VAT auto-populated return.
Step by step: a monthly VAT and eTIMS review
- Close the period in your ERP and list output VAT (sales) and input VAT (purchases), with invoice numbers, dates, PINs, taxable value and VAT.
- Compare those sales with eTIMS revenue (sales invoices and credit notes recorded in eTIMS for the period).
- Compare those purchases with eTIMS expenditure (supplier eTIMS invoices that carry your PIN, plus credit notes).
- Compare both sides with the iTax VAT data for the same period. VisionONE connects to KRA through GavaConnect APIs to bring in iTax VAT data and withholding tax certificates (paid and received) for reconciliation. Your authorised team still verifies the auto-populated VAT figures before filing.
- Investigate differences: missing transmissions, credit notes, invoice dates, invoices that are not yours, and input VAT that may not be allowable.
- Review withholding tax certificates you have paid (issued) and received, and keep them with the period pack.
- Your authorised filer confirms the return and files it on iTax. Preparing a reconciliation does not file the return.
Input and output VAT
Output VAT is the VAT on your taxable sales. Input VAT is the VAT on eligible purchases. Reconcile each side separately, then review the net figure. A purchase recorded in the ERP is not automatically an allowed input-VAT claim. Check invoice support, the buyer PIN and the rules that apply to that purchase.
eTIMS revenue and eTIMS expenditure
eTIMS revenue here means your sales invoices and credit notes in eTIMS for the period. eTIMS expenditure means supplier invoices and credit notes that appear in eTIMS against your PIN. Match them to the ERP sales and purchase records, then explain any item that appears on only one side.
Withholding certificates paid and received
Keep a register of withholding tax you have deducted and remitted (certificates paid or issued) and of certificates you have received from customers or other payers. Match each certificate to the supplier or customer, the period, the amount and the remittance evidence. A software record does not replace a KRA-issued certificate.
Where VisionONE helps
VisionONE helps finance teams reconcile VAT, revenue, and expenses against eTIMS records and investigate discrepancies. VisionONE connects to KRA through GavaConnect APIs to bring in iTax VAT data and withholding tax certificates (paid and received) for reconciliation. GavaConnect is KRA’s official Enterprise API platform (developer portal: developer.go.ke). It prepares VAT, PAYE and withholding records from the transactions already in the ERP, and it keeps certificate follow-up visible for your reviewer. See tax reporting and KRA workflows.
What VisionONE does not do
- VisionONE does not file VAT or other returns on iTax automatically. Your authorised team reviews the figures and files the return on iTax.
- VisionONE is not a KRA-approved third-party eTIMS integrator and does not claim KRA certification.
- This GavaConnect connection is for iTax VAT data and withholding tax certificates. It is not a “KRA eTIMS API.” For invoices you raise in VisionONE, use eTIMS-ready invoicing.
For connecting invoices you raise in VisionONE to eTIMS, see KRA eTIMS integration and how to integrate your ERP with KRA eTIMS.
FAQ
What is an auto-populated VAT return?
KRA describes the auto-populated VAT return as a filing process where VAT figures are pre-filled from information in iTax, TIMS, eTIMS and customs systems. VAT-registered taxpayers still have to verify and confirm the accuracy of the return before filing.
How do I reconcile eTIMS invoices with my VAT return?
List input and output VAT from your books, compare sales with eTIMS revenue and purchases with eTIMS expenditure, then compare both with the auto-populated VAT figures in iTax for the same period. Investigate differences before your authorised filer submits the return.
How should withholding tax certificates be reviewed?
VisionONE connects to KRA through GavaConnect APIs to bring in withholding tax certificates (paid and received) for reconciliation. Review each certificate against the person, period, amount and remittance evidence. A software record does not replace a KRA-issued certificate.
Does VisionONE file the VAT return on iTax?
No. VisionONE helps finance teams reconcile VAT, revenue, and expenses against eTIMS records and investigate discrepancies. Your authorised team reviews the figures and files the return on iTax.
Is VisionONE a KRA-approved eTIMS integrator?
No. VisionONE is an ERP vendor. It is not a KRA-approved third-party eTIMS integrator and does not claim KRA certification. eTIMS integration for invoices raised in VisionONE is offered as an add-on, confirmed in your proposal.