Accounting · Tax

The supplier gets the net. The tax waits in its own account.

Set a withholding rate on each supplier and every bill from them carries it. The balance due is net of the deduction, so payments pay the net, and each payment books its share of the deduction in the month it was made. At month end the register says what to remit, exports a CSV for the return and prints a certificate per supplier.

Start free Follow one bill to the remittance

Income-tax and VAT withholding · Booked as each payment lands · Monthly register · CSV export · Certificate PDF · Customer-withheld payments

BILL-0102 · Kilimani AdvisoryApproved

Subtotal, before VAT250,000.00

VAT 16%40,000.00

Bill total290,000.00

Withholding 5% of the subtotal12,500.00

Balance due to the supplier 277,500 What the pay screens and payment runs pay.

Withholding tax payable 12,500 Booked share by share as the bill is paid, cleared when you remit.

Before VATthe deduction is the rate times the bill’s subtotal, for income-tax and VAT withholding alike

Each paymentbooks its share of the deduction, dated when it was made — so a bill paid across two months reports in both

Per suppliera tax PIN and a default rate, which each new bill copies and can override

Never overa remittance above what was withheld and not yet remitted for the month is refused

Why it goes wrong on a spreadsheet

Withholding is money you hold for someone else. It needs somewhere to sit.

When you pay a consultant and withhold tax, two things are true at once: you owe the consultant less, and you now owe the tax authority. Done by hand, the first half usually happens — someone types a smaller figure into the bank — and the second half lives in a spreadsheet that has to be rebuilt every month from bank statements.

Here the bill carries both halves. The rate comes from the supplier, the deduction is calculated on the bill, the payable to the supplier is net of it, and as each payment is confirmed its share of the deduction moves into Withholding Tax Payable. The month’s register is then a report of what the books already say, not a reconstruction.

Both directions

What you withhold, and what is withheld from you.

You deduct · a liability

From supplier bills

You set up the rates your organization applies — a name, a percentage and whether it is income tax or VAT — and give each supplier a default.

A bill copies the supplier’s default rate and can be given another, or none.
The amount is the rate times the subtotal before VAT, rounded to the cent.
The balance due is net of it, so pay screens and payment runs never pay it to the supplier.
Booked in step with each confirmed payment or debit note applied: Dr Accounts payable, Cr Withholding tax payable, for that settlement’s share.
Remitted from the monthly register: Dr Withholding tax payable, Cr the account it was paid from.

They deduct · an asset

From your invoices

A customer who withholds from your invoice pays you less and hands you a certificate. Recording that difference as an unpaid balance is how receivables fill up with amounts nobody will ever pay.

Record it on the invoice as a payment by the method “withheld by customer”.
Put their certificate number in the reference.
It settles the invoice like any payment, but to Withholding Tax Recoverable rather than the bank.
The month’s register totals what customers withheld, beside what you deducted.

From rate to remittance

Six steps, and you type a figure in only one of them.

Once · Set up

Rates, then suppliers

Create the rates your organization uses, each income tax or VAT. Give each supplier their tax PIN and a default rate, on the web or in the mobile app. A rate can be retired without touching the bills that used it.

Each bill · Capture

The bill calculates the deduction

The supplier’s rate is applied to the subtotal, and the balance due is the total less the deduction. Bills a supplier submits from the vendor portal pick up their default rate the same way.

Each bill · Pay

Payments pay the net

Pay it by hand or in a payment run — either way the most that can be paid is the net balance.

Each payment · Book

The deduction moves to the liability

Each confirmed payment, and each debit note applied to the bill, books its share of the withholding — the deduction times what it settled over the bill’s net — dated when it happened, and that date places it in a month’s register. The last settlement makes the total exact; a payment that fails after it was confirmed takes its share back.

Month end · Report

Register, CSV and certificates

The register lists the month’s deductions bill by bill, with totals by kind, what customers withheld and what has been remitted. Export it as a CSV for the return, and print a certificate for each supplier.

Month end · Remit

Pay it over

Record the amount, the date, the bank account and the payment reference against the month and the kind. This is the one figure you type — and it is refused if it is more than was withheld and not yet remitted.

Worked example

One consultancy bill, paid across two months, remitted twice.

A Nairobi organization engages an advisory firm. The rates are illustrative — your workspace holds whatever rates you set up. Amounts in KES.

BILL-0102 from Kilimani Advisory LLP

Their invoice INV-2210, dated 3 October. The supplier’s default rate is “Professional fees 5%”, kind income tax. No purchase order: approving the bill posts its own journal.

Consultancy, subtotal250,000.00

VAT 16% of 250,00040,000.00

Bill total290,000.00

Withholding 5% of 250,000− 12,500.00

Balance due to the supplier277,500.00

Approved, 3 Oct expense bill journal

DrProfessional fees250,000

DrInput tax40,000

CrAccounts payable290,000

Payment, 10 Oct 150,000 by bank · share 12,500 × 150,000 ÷ 277,500

DrAccounts payable6,756.76

CrWithholding tax payable6,756.76

DrAccounts payable150,000

CrBank150,000

Payment run, 6 Nov the remaining 127,500 · the rest of the 12,500

DrAccounts payable5,743.24

CrWithholding tax payable5,743.24

DrAccounts payable127,500

CrBank127,500

Remitted, 18 Nov for October, income tax

DrWithholding tax payable6,756.76

CrBank6,756.76

Remitted, 15 Dec for November, income tax

DrWithholding tax payable5,743.24

CrBank5,743.24

Recording the full 12,500 for October income tax is refused: only 6,756.76 was withheld and not yet remitted for that month. The other 5,743.24 was booked on 6 November and belongs to November’s return.

Where every shilling ended up

Three accounts after both remittances. Accounts payable and withholding tax payable both come back to zero; the bank paid out the full bill total, in two directions.

Accounts payable · Kilimani Advisory

Withholding, 10 Oct6,756.76

Payment, 10 Oct150,000

Withholding, 6 Nov5,743.24

Run, 6 Nov127,500

Bill, 3 Oct290,000

Debits 290,000 · Credits 290,000Balance 0

Withholding tax payable

Remitted, Oct6,756.76

Remitted, Nov5,743.24

Booked, 10 Oct6,756.76

Booked, 6 Nov5,743.24

Balance0

Bank

10 Oct150,000

6 Nov127,500

18 Nov6,756.76

15 Dec5,743.24

Paid out290,000

To the supplier277,500

To the tax authority12,500

Bill total290,000

The other direction, same month

A county client withholds VAT from your invoice

You invoice 100,000 plus 16,000 VAT, a total of 116,000. The client withholds VAT at an illustrative 2% of 100,000 — that is 2,000 — and pays 114,000 with a certificate.

Record 114,000 as the bank payment it was.
Record 2,000 as withheld by customer, with the certificate number as the reference.
The invoice closes at zero, and the 2,000 sits in Withholding Tax Recoverable rather than in receivables.

What you enter, what is calculated

The customer’s figure is yours to enter

On supplier bills the deduction is calculated from the rate. On the customer side you record the amount on their certificate, because it is their calculation, not yours.

Supplier side: rate times subtotal, on the bill.
Customer side: the certificate amount, as a payment.
Remittance: the amount you paid over, checked against the month.

The monthly register

October, as the return needs it.

One row per payment’s share, placed in the month that payment was made — so the advisory bill shows only its October share here, and the rest appears in November. These are the CSV’s own columns. The second bill here is a cleaning contractor carrying an illustrative 2% VAT withholding rate.

Withholding tax · October 2026

Export for the return Certificate per supplier Record a remittance

Supplier PIN	Supplier	Invoice number	Invoice date	Taxable value	Rate %	Tax withheld	Kind	Deducted on
P051234567X	Kilimani Advisory LLP	INV-2210	2026-10-03	135,135.20	5	6,756.76	Income tax	2026-10-10
P052345678Y	Tana Facility Services	TFS-0931	2026-10-06	60,000.00	2	1,200.00	VAT	2026-10-15

Income tax withheld6,756.76

VAT withheld1,200.00

Withheld by customers2,000.00

Outstanding to remit7,956.76

The supplier certificate

A statement your supplier can reconcile against.

Suppliers ask for proof of what was withheld, usually at the moment they notice a payment was short. The certificate is a PDF per supplier, per month, listing every deduction from their bills: invoice number, date, taxable value, rate and amount.

It names both parties and both PINs. Your organization’s PIN comes from the employer PIN in HR settings, or your eTIMS PIN if that is empty, and the supplier’s from their record.

It says plainly what it is: a statement of the deductions in your books. The tax authority’s own certificate, issued when the tax is remitted, is the one your supplier claims against — and nothing on this page pretends otherwise.

Withholding tax certificate

Period: October 2026

Deducted by: Your organization · PIN P000000000A
Deducted from: Kilimani Advisory LLP · PIN P051234567X

Invoice	Date	Taxable	Rate	Withheld
INV-2210	03 Oct	135,135.20	5%	6,756.76

This statement lists the deductions in our books. The tax authority’s own certificate, issued when the tax is remitted, is the one to claim against.

What holds it together

Small rules that keep the liability honest.

PIN and rate on the supplier

Set once on the supplier, on the web or in the mobile app, and carried onto every new bill.

Two kinds, any rate

Rates are income tax or VAT, held to three decimal places, and can be retired without rewriting old bills.

Booked in step with payment

Each confirmed payment or applied debit note books only the share it earned, whichever route it came by. A repeated confirmation books nothing more, and the last settlement makes the total exact.

Runs pay the net

Because the balance due already excludes the deduction, a payment run cannot pay it to the supplier by mistake.

Remittance capped

A remittance is checked against what was withheld and not yet remitted for that month and kind.

CSV for the return

Supplier PIN, supplier, invoice number and date, taxable value, rate, tax withheld, kind and the date deducted — one row per payment’s share.

Certificate per supplier

A monthly PDF of what was deducted from one supplier, bill by bill, with both PINs.

Customer-withheld payments

Settle an invoice to Withholding Tax Recoverable with the certificate number on record, and see the month’s total in the register.

In the mobile app

The register, the rates and recording a remittance are in the AWRA mobile app as well as on the web, over the same API.

The straight answer

What AWRA OpsHub does today

Withholding rates of two kinds, income tax and VAT, set up by you and retired when no longer used.
A tax PIN and a default rate on each supplier, copied onto every new bill and changeable per bill.
The deduction calculated on the bill as the rate times the subtotal before VAT, with the balance due net of it.
Booking in step with what settles the bill — each confirmed payment and each debit note applied books its share, dated when it happened, from every route a supplier payment can take.
A payment that fails after it was confirmed takes its share back, and a remittance recorded in error can be reversed so the month is outstanding again.
A monthly register of supplier deductions by the date each share was booked, totals by kind, what customers withheld and what was remitted.
Remittances posted against the bank account they were paid from, refused above what is outstanding for the month and kind.
A CSV export of the month’s deductions, one row per payment’s share.
A certificate PDF per supplier per month, with both PINs.
Customer-withheld payments that settle an invoice to Withholding Tax Recoverable, with the certificate number as the reference.
The register, rates and remittance in the mobile app, over the same API.

More we can add to your workspace

A direct connection to the tax authority’s filing system, so the month’s deductions are submitted from the register rather than exported.
The authority’s own return template, such as the iTax withholding schedule, filled straight from the register instead of from the general CSV.
Withholding on a payment made against a purchase order without a bill, using the order’s value as the base.
The customer’s certificate attached to the invoice it settled, as a file alongside the certificate number.
PIN format checks per country, so a mistyped supplier PIN is caught on the supplier record.
Income-tax and VAT withholding together on one bill, for suppliers who are subject to both.
Thresholds that apply a rate only above an amount per bill or per period.

Where we point you to a specialist

We will not decide which rate applies to a supplier. Whether a payment is a professional fee, a contractual fee or exempt is a judgement for you and your tax adviser. The system applies the rate you choose, exactly and every time.
We will not present our statement as the authority’s certificate. The PDF lists the deductions in your books and says so on its face; the certificate that counts is the one the authority issues when the tax is remitted.

The authority’s own return template is the item in that middle column that saves the most time at each month end, and a filing connection is the one that removes the step altogether. Tell us which authority you file with and how you file today, and we will come back with a written spec, a timeline and a price.

Around the deduction

Where withholding meets the rest of the books.

Supplier bills and payablesThe bills that carry the deduction, and the payment runs that pay the net. Vendor paymentsThe confirmed payment whose arrival books the withholding. General ledgerThe journal behind every line in the worked example above. KRA eTIMS and taxInvoice filing at issue, and the PIN your certificate falls back to. Payroll compliancePAYE and the statutory payroll files, which live with HR rather than here. Accounting automationThe finance hub this sits in, from chart of accounts to statements.

Frequently asked questions

How is the withholding on a supplier bill calculated?

It is the bill’s withholding rate times its subtotal before VAT, rounded to the cent — the same base for income-tax and VAT withholding. The rate is the supplier’s default unless you choose another on the bill, or none. The bill’s balance due is the total less the deduction, so the pay screens and payment runs pay only the net to the supplier.

When is the withholding booked to the ledger?

In step with what settles the bill. Each confirmed payment, and each debit note applied to it, books its share — the withholding times what it settled over the bill’s net — as a debit to accounts payable and a credit to withholding tax payable, dated when it happened. A bill paid half in October and half in November reports half in each month’s register, and the last settlement makes the total exact. A payment that fails after it was confirmed takes its share back. Booking at payment rather than at the invoice follows the point at which the obligation to withhold arises.

What does the monthly register show?

Every supplier deduction booked in the month, one row per payment’s share with the supplier’s PIN, invoice number and date, taxable value, rate, amount and kind; the totals by kind; what customers withheld from your invoices that month; what has been remitted; and what is still outstanding. From there you export the CSV, print supplier certificates and record the remittance.

Is the CSV the official return template?

It is a general CSV of the month’s deductions, with the columns a withholding return asks for, which you use to prepare the return in your authority’s own format. Filling the authority’s template directly, such as the iTax withholding schedule, is something we can add to your workspace.

Is the certificate PDF the official withholding certificate?

It is a statement of the deductions in your books for one supplier and one month, naming both organizations and both PINs, and it says so on its face. The certificate your supplier claims against is the one the tax authority issues when the tax is remitted.

How do we record a customer withholding from our invoice?

Record the amount they paid as a normal payment, then record the amount they withheld as a payment by the method “withheld by customer” with their certificate number as the reference. It settles the invoice like any payment, but to Withholding Tax Recoverable rather than to the bank, so the invoice closes and the tax sits where it can be claimed.

What stops us remitting the wrong amount?

A remittance is recorded against a month and a kind, and it is refused if it is more than was withheld for that month and kind and not yet remitted. It posts as a debit to withholding tax payable and a credit to the bank account you paid from, and one recorded in error can be reversed, which makes the month outstanding again.

Does this cover PAYE on salaries?

No — PAYE is calculated and filed in the HR and payroll module, alongside the other statutory payroll files. This page covers withholding on supplier bills and withholding by your customers.

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