CONTPAQi Nóminas: ISR Calculation and Employment Subsidy Withholding Errors

March 23, 2026

10 min read

Fresh

TL;DR — Quick Summary

Fix ISR errors in CONTPAQi Nóminas: outdated SAT tax tables, negative employment subsidy, annual ISR adjustment, and extraordinary payment withholding issues.

ISR Calculation Errors in CONTPAQi Nóminas

Mexico’s Impuesto Sobre la Renta (ISR) — income tax withheld from employee wages — is governed by Art. 96 of the LISR and involves layered calculations: monthly progressive tax tables, employment subsidy offsets, exempt income limits, and an annual true-up in December. CONTPAQi Nóminas automates all of this, but when tax tables are stale or concepts are misconfigured, withholding errors ripple across every payroll run. This guide walks through the root causes and their fixes.

The Error

Common symptoms include:

ISR withheld in the payroll receipt does not match a manual calculation using published SAT tables.
The system displays “Error en cálculo de subsidio al empleo” when processing payroll.
Employment subsidy shows as a negative value or zero for low-income workers who should receive it.
Extraordinary payments (aguinaldo, PTU, vacation premium, severance) produce unexpectedly high or low ISR withholding.
The annual ISR adjustment in December creates large, unexpected charges for workers.
The Earnings and Withholding Certificate does not reconcile with the employer’s annual declaration.

Root Cause

1. Outdated ISR tables

Every January, SAT publishes updated ISR tables and rates in the DOF for monthly withholding (Art. 96 LISR) and the annual adjustment table used in December. If CONTPAQi was not updated at the start of the fiscal year, it uses last year’s brackets and rates, producing systematically incorrect withholding.

2. Employment subsidy table errors

The employment subsidy table was established in the Decree of December 11, 2013 and has not been formally revised, but it must be entered precisely. A single missing bracket or a typo in a peso amount causes the calculation to fail for workers in that income range, producing either zero subsidy or the error message.

3. Exempt income concepts misconfigured

Art. 93 LISR exempts specific income types up to defined limits. If payroll concepts do not have the correct SAT income type code and exemption percentage configured, CONTPAQi taxes income that should be exempt, resulting in over-withholding.

4. UMA and minimum wage not updated for the year

The UMA (Unit of Measure and Update) and the General Minimum Wage change each year and serve as the basis for all Art. 93 exemption calculations. Stale values shift every exemption threshold, compounding errors across the entire payroll.

Step-by-Step Solution

Step 1 — Update the ISR tables for the current fiscal year

Go to Configuration > Tax Parameters > ISR Tables and Rates.
Select the current fiscal year.
Compare each bracket’s lower limit, fixed quota, and marginal rate against the DOF publication for the current year.
If values are from the prior year, apply the system update from the CONTPAQi portal or enter the eight brackets manually.

Pay special attention to the lower limit of the first bracket and the rates for middle brackets, where the majority of minimum-wage and mid-salary workers fall.

Step 2 — Correct the employment subsidy table

Go to Configuration > Tax Tables > Employment Subsidy.
The table must match Annex 8 of the current Miscellaneous Tax Resolution (RMF) exactly.
Verify monthly subsidy amounts in the right-hand column to the centavo.
If a worker’s monthly salary is at a bracket boundary, a one-peso error in the table can eliminate subsidy entirely.

Step 3 — Update UMA and minimum wage values

In Configuration > Fiscal Year Values, enter:
- Daily and monthly UMA for the current year (published in the DOF each February).
- General Minimum Wage for the applicable geographic zone.
These values drive all Art. 93 LISR exemption calculations.

Step 4 — Review exempt income concept configuration

In Catalogs > Concepts, verify each exempt income type:

Concept	SAT Code	Art. 93 Exemption Limit
Social welfare (previsión social)	019	Up to 1× monthly minimum wage for min-wage earners; or 90% for others
Savings fund (fondo de ahorro)	015	Up to 1.3× annual minimum wage (employer contribution)
Food vouchers (vales de despensa)	023	Up to 40% of monthly UMA
Overtime	006	First 9 weekly hours at 50%, capped at double minimum wage
Aguinaldo	002	30 days of UMA annually
Vacation premium	022	15 days of UMA annually

Step 5 — Verify ISR on extraordinary payments

For aguinaldo, PTU, vacation premium, and severance, Art. 96 LISR prescribes a specific method:

Determine the worker’s ordinary monthly income.
Add the taxable portion of the extraordinary payment (gross amount minus exemption).
Calculate ISR on the combined total using the monthly table.
Subtract the ISR that would apply to ordinary income alone.
The difference is the additional ISR to withhold on the extraordinary payment.

CONTPAQi performs this automatically if concepts have the correct SAT extraordinary income type. If results are wrong, confirm the concept is not flagged as ordinary monthly income.

Step 6 — Process and review the December annual ISR adjustment

In the December payroll, go to Period Parameters > Annual ISR Adjustment and enable it.
CONTPAQi will calculate for each worker:
- Annual ISR owed: using the annual table on total taxable income for the year.
- Cumulative ISR withheld: sum of all monthly withholdings.
- Difference: withheld additionally or refunded depending on the sign.
Review the Annual Adjustment Report before stamping. Workers with variable income (commissions, bonuses) typically show larger differences.

Alternative Solution

If a system update is not immediately available, you can manually enter the ISR tables under Configuration > Tables and Rates. Download Annex 8 of the current RMF from sat.gob.mx and enter the values directly. This is a temporary workaround — apply the official update as soon as it is released to maintain reporting consistency.

Prevention

Update CONTPAQi Nóminas every January before processing the first payroll of the fiscal year.
Set an annual reminder to update the UMA (published each February) and minimum wage (published in December/January).
Before processing the December payroll, run a test calculation (without stamping) to preview annual ISR adjustments.
Keep a signed PDF copy of the SAT’s ISR tables for each year as audit documentation.
Periodically verify the Earnings and Withholding Certificate for at least two representative workers (minimum wage and mid-salary) against a manual calculation.

Negative ISR for minimum-wage workers

When the employment subsidy exceeds the ISR owed, the net result is no withholding and, in some cases, the employer must deliver the subsidy as an additional cash payment to the worker. CONTPAQi should reflect this as “subsidy delivered” in the CFDI, not as negative ISR. If negative ISR appears, the subsidy concept is misconfigured.

Discrepancy between CFDI ISR and the employer’s annual declaration

Total ISR withheld across all payroll CFDIs for the year must match the employer’s annual informative wage declaration. Discrepancies above 1% can trigger SAT audit flags. Use the Accumulated ISR by Worker report to reconcile before filing.

”Worker has no ISR table assigned” error

This occurs when a worker’s payroll type or tax regime has no table linked. Verify that the worker’s profile has the “Wages and Salaries” regime assigned and that an ISR table is linked to that regime in fiscal parameters.

Summary

ISR tables and the employment subsidy table must be updated at the start of each fiscal year.
UMA and minimum wage values are the foundation of all Art. 93 LISR exemption calculations.
Extraordinary payments (aguinaldo, PTU, vacation premium) use a special Art. 96 method that adds the taxable portion to ordinary monthly income to determine the marginal rate.
The December annual ISR adjustment compares cumulative monthly withholdings against annual ISR owed; the difference is collected or refunded in the final paycheck.
Employment subsidy should never be negative; if it appears negative, there is a configuration error in the subsidy table or income brackets.
Reconcile CFDI withholding totals with the employer’s annual declaration before filing with SAT.

Guide & Instructions

Estimated Time: 30m

Tools Needed:

CONTPAQi Nóminas

Verify and update the fiscal year ISR tables

Go to Configuration > Tax Parameters > ISR Tables and Rates. Confirm the Art. 96 LISR tables match the current fiscal year as published in the DOF. If outdated, download the update from the CONTPAQi portal or enter the values manually.

Update the employment subsidy table

In Configuration > Tax Tables > Employment Subsidy, verify that income ranges and subsidy amounts match the current SAT table. Each bracket boundary must be exact — a one-peso error can eliminate subsidy for an entire income range.

Configure exempt income limits for workers

In Catalogs > Concepts, review each exempt income concept. Verify that social welfare, savings fund, and food voucher concepts have the correct SAT income type and exemption limits per Art. 93 LISR using the current UMA and minimum wage values.

Calculate and verify ISR on extraordinary payments

For aguinaldo, PTU, vacation premium, and severance, confirm that concepts are configured with the correct SAT extraordinary income type. Run a test calculation and compare against the Art. 96 LISR method: add the taxable extraordinary amount to ordinary monthly income, calculate ISR on the total, then subtract the ISR on ordinary income alone.

Run the annual ISR adjustment in December

In the December payroll period, enable Annual ISR Adjustment in Period Parameters. CONTPAQi will calculate the difference between annual ISR owed and total monthly ISR withheld. Review the Annual Adjustment report for each worker before stamping the CFDIs.

Reconcile CFDI withholding against the employer's annual declaration

Generate the Earnings and Withholding Certificate report per worker. Total ISR withheld across all payroll CFDIs for the year must match what is reported in the employer's annual informative wage declaration filed with SAT.

Frequently Asked Questions

Why does CONTPAQi's ISR calculation differ from a manual calculation using SAT tables?

The most common cause is that the ISR tax tables for the current fiscal year have not been updated in CONTPAQi. Check under Configuration > Tax Parameters that the Art. 96 LISR tables match the current year as published in Mexico's Official Gazette (DOF).

What causes the 'Error en cálculo de subsidio al empleo' message in CONTPAQi?

This error means the employment subsidy table is outdated or the worker's income falls outside any defined range. Update the table under Configuration > Tax Tables > Employment Subsidy and verify that the monthly salary is correctly entered in the worker's profile.

How is ISR calculated on aguinaldo (Christmas bonus) in CONTPAQi Nóminas?

Aguinaldo has an exemption of 30 days of UMA. The taxable portion is added to the month's ordinary income and the Art. 96 LISR monthly rate is applied. CONTPAQi handles this automatically if the payroll concept is configured with SAT income type 002 and the correct exemption code.

When is the annual ISR adjustment processed in CONTPAQi Nóminas?

The annual ISR adjustment runs during the December payroll (last period of the fiscal year). CONTPAQi compares the annual ISR owed (using the annual table) against the total ISR withheld monthly throughout the year. Any difference is either withheld from or returned to the employee in the final paycheck.