Three different audits go by the same name in Switzerland. Find out below which one concerns you, what gets checked, the records to gather and the control points.
Reading time: 17 min
A Geneva SME of 40 employees receives a letter from its compensation fund announcing an audit. An industrial company of 120 people in Neuchâtel discovers that it has to analyze its pay gap between women and men. A finance director simply wants to check the statements before the year-end close. All three talk about a "payroll audit", and not about the same thing.
These three situations do not call for the same moves. The first audit is one you undergo: your compensation fund carries it out at your premises. The second follows from a legal obligation tied to your headcount. The third, you decide on.
This article first separates these three audits, then goes into detail on the one you choose: scope, records to gather, control points item by item, rhythm and cost. For the regulatory framework itself, our guide to payroll compliance and regulations in Switzerland remains the way in.
In brief
- Work out first which audit is being discussed: the one your compensation fund carries out at your premises, the one the law imposes above a certain headcount, or the one you decide to run.
- Do not expect any fixed rhythm for the employer audit: the deadlines depend on your situation, and only your fund can tell you yours.
- Audit your data before your calculations: a wrong activity rate produces a difference that repeats every month.
- Reconcile payroll and accounting at every close: a discrepancy found in January gets corrected, the same discrepancy found three years later gets discussed with an authority.
Three different audits go by the same name
The word audit covers three exercises that share neither the same trigger, nor the same scope, nor the same consequences. Knowing which one is being discussed saves you from preparing the wrong file.
The audit by your compensation fund
This audit covers the salaries you have declared and the contributions that follow from them. You set neither its principle nor its date: your fund announces it, and then an auditor examines your records. A Fribourg construction company that has been declaring salaries for four years falls within this scope, without having done anything wrong.
The equal pay analysis
This analysis does not depend on a letter received, but on your headcount at the start of a year. It ignores your deadlines and your contribution rates: it statistically compares the salaries of the women and the men in your company. A Vaud IT services company going from 90 to 105 employees changes category without any authority warning it.
The internal payroll audit
The third audit is a choice, with no imposed form and no report to file. Its value fits in one sentence: it is run when you want, and therefore before the other two. A hotel group that has just taken over an establishment in Zermatt launches one to find out what it has taken on.
The employer audit: what gets checked
This audit takes place at your premises, on your records. Two questions always come up: when does it fall, and what does it cover.
One rule is set out in black and white in the federal circular: a company is audited at the latest four years after it was set up if its total salaries exceed CHF 150,000.
Source: Federal Social Insurance Office, circular on employer audits (CCE) 318.107.08, version 7, as at 1 June 2026, verified on 12 August 2026.
A second rule concerns doubtful situations: where certain elements suggest irregularities in the reporting, the fund carries out an audit within a maximum of five years, and at the latest within the shortest applicable deadline.
Source: Federal Social Insurance Office, circular on employer audits (CCE) 318.107.08, version 7, as at 1 June 2026, verified on 12 August 2026.
Common misconception
No official text says that every employer is audited every four or five years. The circular sets deadlines by category of employer and by triggering element, by means of a conversion table. The two rules above are the two the circular actually states. For your own deadline, ask your fund.
What the auditor examines
The official documentation publishes no list of control points, and we will not invent one. One verifiable element is enough to grasp the logic of the exercise: the final contributions are set on the basis of your salary declaration, submitted at the latest on 30 January following the end of the contribution year, failing which late-payment interest is due on any difference.
Source: AVS/AI Information Centre, memento 2.01, Contributions to AVS, AI and APG, as at 1 January 2026, verified on 12 August 2026.
The first subject of an audit is therefore the gap between what your accounts show and what your declaration states. A monthly representation allowance paid to a sales director in Lugano, booked as an expense but never made subject to contributions, shows up in that reconciliation.
The records you must be able to produce
An audit is prepared with documents, not with explanations. Gather, over the whole period announced:
- the payroll journal and the individual statements for each employee;
- the salary certificates given to employees and to the tax authorities;
- the employment contracts, the amendments and the exit letters;
- the contribution statements and the annual salary declarations;
- the general accounts, in particular the personnel costs;
- the expense receipts and the applicable expense regulations.
These records are not thrown out after three years. The books and accounting records, as well as the annual report and the audit report, are kept for ten years, a period that runs from the end of the financial year.
Source: Swiss Confederation, Code of Obligations (CO), RS 220, art. 958f, version in force on 1 January 2026, verified on 12 August 2026.
What follows an audit
The audit ends with a set of findings that affect your current account. The adjustment mechanism is a known one: if the instalments paid exceed the final contributions, the difference is refunded to you, and if they fall short, you receive an invoice. A correction of declared salaries also changes your future instalments, because funds set them on the estimated total of salaries and you must inform them when that total changes significantly.
Source: AVS/AI Information Centre, memento 2.01, Contributions to AVS, AI and APG, as at 1 January 2026, verified on 12 August 2026.
A mechanical workshop in Valais that regularizes two years of gratifications therefore has two things to do, not one.
The equal pay analysis: who is concerned
This obligation catches out fast-growing companies, because it does not announce itself. It is triggered by a headcount, it repeats over time, and it ends with written information to your employees.
The headcount threshold
Employers with a headcount of at least 100 employees at the start of a year carry out an internal equal pay analysis for that same year. Apprentices are not counted in that headcount. The analysis is repeated every four years, and an employer whose analysis shows that equal pay is respected is released from the obligation to repeat it.
Source: Swiss Confederation, Federal Act on Gender Equality (LEg), RS 151.1, art. 13a, version in force since 1 July 2020, verified on 12 August 2026.
The horizon of this obligation has a date. The Federal Office for Gender Equality states that employers can in principle be subject to it until 30 June 2032 if they reach the threshold of 100 people employed at the start of a year.
Source: Federal Office for Gender Equality, Promoting equal pay with Logib, verified on 12 August 2026.
The analysis method
The analysis rests on a statistical comparison, and the Federal Office for Gender Equality devotes a whole page to its Logib tool. We do not set out that method, which belongs to that office.
The point that concerns you sits upstream: an analysis is worth what the data you feed it is worth. An activity rate wrongly entered for a nurse at 80% in Delémont, a role left under its former title after a promotion, and the comparison is made on salaries that do not compare.
The verification and informing employees
The analysis does not stay in your hands. Employers subject to the Code of Obligations have their analysis verified by an independent body, at their choice an approved audit firm, an organization within the meaning of art. 7 of the act, or an employee representation. They then inform employees in writing of the result, at the latest one year after the verification, and listed companies publish that result in the notes to their annual report.
Source: Swiss Confederation, Federal Act on Gender Equality (LEg), RS 151.1, art. 13d, 13g and 13h, version in force since 1 July 2020, verified on 12 August 2026.
That chain takes several months, which rules out handling it just before a year-end close.
Running your own audit: where to start
Auditing your payroll means ranking risks, not re-reading everything. In an SME, the three that come up most often are a poorly kept data transmission process, a contribution base frozen for years, and a cantonal attachment never rechecked. The rest of the work consists in bounding the exercise so that it fits the time you can give it.
An internal audit can be run with your own teams, with your fiduciary or with your payroll provider. When the production of the statements is entrusted to a third party, as the payroll management solutions from Numeriq Payroll provide for, the object of your checking shifts: it bears less on the calculation itself than on the data you send and on the reconciliations only you can make.
Defining the scope and the period
An audit with no written scope spreads out and never ends. Set three boundaries: the entities concerned, the period covered and the populations examined.
A cleaning company whose teams work in Geneva and in the canton of Vaud does not have the same subject depending on where each person works. Start with a short and complete period, for example the last twelve closed months.
Gathering the records
The records for an internal audit overlap with those for an employer audit, with one addition: your internal rules. Add the staff regulations, management's decisions on bonuses, the applicable collective labor agreement if your sector has one, and the settings of your payroll software.
This phase already reveals discrepancies, before any calculation, and a payroll compliance checklist helps you leave out no category of document.
Choosing between a full check and a sample
The full check is justified on the at-risk populations: the arrivals and departures of the year, the employees subject to withholding tax, the managers whose pay includes variable elements. A sample is enough on a stable population, for example monthly-paid employees on the same rate for three years.
One rule simplifies the decision: as soon as an anomaly appears in a sample, widen the sample until you find the origin of the error.
The control points, item by item
This section reads as a verification list. It does not describe the errors themselves: our article dedicated to the most common payroll errors explains what each check is trying to catch.
Personnel data
Wrong data produces an error that repeats at every cycle, which makes it the first item to check. Take each employee's file and compare it against the payroll software:
- the signed contract, its amendments and the activity rate applied;
- the start and end dates, with the pro rata calculations;
- the residence or work permit, valid and in force;
- the place of work and the canton of residence;
- the family situation that creates entitlement to family allowances;
- the employee's bank details.
Salary components
Every line of a statement must trace back to a written decision. Check that the base salary matches the contract, that the thirteenth salary applies to the right base and the right pro rata, that overtime rests on an approved time record, and that bonuses correspond to a management decision or to a contractual clause.
Benefits in kind deserve the same attention: a company car assigned to a sales representative in Basel or accommodation made available each follow their own treatment rule.
The contribution bases
The starting point is not open to discussion. The determining salary is the salary on which contributions are levied, and it includes, among other things, bonuses, compensation for overtime, stand-in work or night work, gratifications, long-service gifts, loyalty or performance bonuses, as well as benefits assessable in money arising from employee participation plans.
Source: AVS/AI Information Centre, memento 2.01, Contributions to AVS, AI and APG, as at 1 January 2026, verified on 12 August 2026.
Check element by element that each one is flagged as subject or not subject in your software. The bases do not overlap from one insurance scheme to another: your pension institution and your accident insurer give you your own parameters.
Withholding tax
The scales vary from one canton to another and are updated regularly, which is why we publish none of them here. Check that every employee concerned is attached to the right canton, that changes of personal situation have been applied in the right month, and that the scale used is the one published by the competent tax authority for the current year. If you are unsure which canton is competent, the Federal Tax Administration maintains the list of the authorities to contact.
Source: Federal Tax Administration, withholding tax, verified on 12 August 2026.
A cross-border sales advisor employed in Basel-Stadt and an Italian manager living in Ticino do not fall under the same attachment.
Declarations and deadlines
The calendar is a control point in its own right, because a delay is penalized regardless of how correct the calculation is. Contributions are paid quarterly where the annual total of salaries does not exceed CHF 200,000, and monthly above that, the final payment deadline always being the 10th day following the end of the quarter or the month.
Source: AVS/AI Information Centre, memento 2.01, Contributions to AVS, AI and APG, as at 1 January 2026, verified on 12 August 2026.
Then take each annual declaration, its sending date and its recipient: our article on salary declarations in Switzerland lists the ones you have to produce.
Reconciliation with the accounts
This final check catches what the previous ones let through. Reconcile the personnel costs in the accounts with the cumulative payroll journal, then explain every discrepancy:
- the clearing accounts are settled after each payment;
- the contributions booked match the funds' statements;
- the provisions for untaken holiday follow a reproducible calculation;
- expense reimbursements are kept distinct from salary components.
How often to audit your payroll
An annual audit is the baseline, but certain events create a risk in the very month they occur. The right rhythm therefore combines a fixed appointment with one-off triggers.
The annual baseline rhythm
Place the full audit before you prepare the annual salary declaration, when the year's data is settled and a correction is still simple. An audit run in November leaves time to put things right on the December payroll.
Add two lighter checks: each month, compare the payroll paid with that of the previous month and explain the differences; each quarter, review the arrivals, the departures and the employees subject to withholding tax.
The events that justify an immediate audit
Some changes alter the mechanics of payroll without warning your processes. Trigger a targeted audit, within the month, in the following cases:
- a change of payroll software or provider, with historical data carried over;
- the arrival of an employee in a new canton;
- the takeover of a company or a team, with its existing contracts;
- the entry into force of a collective labor agreement extended to your sector, or its revision;
- crossing the headcount threshold for the equal pay analysis;
- growth in payroll that moves your contributions to the monthly rhythm;
- the announcement of an audit by your compensation fund.
What makes the cost of a payroll audit vary
No official rate exists for a payroll audit, and we publish none either: the price is built each time on the real volume of work. That volume depends on four parameters, which are also the four questions to ask before requesting a quotation:
- the headcount and the variety of situations: fifty monthly-paid employees on the same status are checked faster than twenty employees mixing part-time work, cross-border commuting and variable elements;
- the number of cantons concerned: each canton adds a tax attachment to check and different counterparties;
- the period covered: one financial year is handled in a single pass, three years mean reconstructing parameters that have changed in the meantime;
- the state of the documentation: filed contracts, approved time records and reconciled accounts shorten an audit, and their absence can lengthen it considerably.
That last point is the one you keep control of: a file kept up to date all year turns an audit into a verification, and a verification costs less than a reconstruction.
Frequently asked questions
How much does a payroll audit cost?
No official source publishes a rate and providers build their offer to measure. Ask for a quotation based on four parameters: your headcount, the number of cantons, the period to be covered and the state of your documentation. Insist on a written scope, because an audit whose extent stays vague always costs more than expected.
Is a payroll audit mandatory in Switzerland?
It depends which one you mean. The audit carried out by your compensation fund cannot be declined, since it is the fund that triggers it. The equal pay analysis is a legal obligation for employers with a headcount of at least 100 employees at the start of a year, apprentices not counted. The internal audit, for its part, remains voluntary.
Source: Swiss Confederation, Federal Act on Gender Equality (LEg), RS 151.1, art. 13a, version in force since 1 July 2020, verified on 12 August 2026.
Who can carry out a payroll audit?
An internal audit is run by your HR or finance function, by your fiduciary, or by your payroll provider. What counts is the independence of whoever checks from whoever produces the statements. That is also why our payroll specialists work from Switzerland, in contact with the funds and the tax authorities the answers depend on.
How long must payroll records be kept?
The Code of Obligations sets ten years for the books and accounting records as well as for the annual report and the audit report, a period that runs from the end of the financial year. Since payroll records feed those books, that period is the safest marker for your archiving.
Source: Swiss Confederation, Code of Obligations (CO), RS 220, art. 958f, version in force on 1 January 2026, verified on 12 August 2026.
What happens if the audit reveals missing contributions?
A contribution that should have been levied does not disappear because it was forgotten: the fund claims payment of it. We publish neither amount nor deadline here, because those elements appear in the decision your fund notifies to you. One point is written in the official documentation: failure to meet the deadline for submitting the salary declaration triggers late-payment interest on any difference.
Source: AVS/AI Information Centre, memento 2.01, Contributions to AVS, AI and APG, as at 1 January 2026, verified on 12 August 2026.
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