VAT Compliance Audit in Geneva for SMEs: Key Points, Common Risks and Process in 2025
Introduction
In a constantly evolving tax environment, managing Value Added Tax (VAT) is a major challenge for SMEs in Geneva and French-speaking Switzerland. With ever more complex rules and increased scrutiny by the Federal Tax Administration (FTA), every company must ensure the compliance of its declarations and internal processes. This article aims to guide executives, financial managers and accountants in preparing for a VAT compliance audit in 2025, based on the expertise of Ark Fiduciaire.
What is a VAT compliance audit and who is concerned?
The VAT compliance audit is an exhaustive review of the application of rules related to VAT collection, declaration and payment. It can be initiated at the request of the FTA or proactively by the business. In 2025, particular emphasis is placed on transparency, transaction accuracy, and the ability to justify all declared amounts.
All companies registered for VAT in Switzerland are concerned, including SMEs and self-employed persons in various sectors (trade, services, cross-border activities, etc.).
Regulatory context in 2025: key points
- The standard VAT rate remains at 8.1% (after the 2024 change), with special rates for certain goods and services.
- Territoriality and exemption rules are evolving, especially for digital services and transactions involving European partners.
- The FTA is increasing risk-based and automated controls (Swissdec procedures, e-invoicing, etc.).
Official sources:
Steps of a VAT compliance audit
1. Internal preparation
- Review of transactions: examine sales and purchase invoices, note applied rates and justification for any exemption or partial liability.
- Check supporting documents: ensure every transaction has valid support (compliant invoice, contract, proof of payment).
- Validate previous declarations: identify any corrections to make before the official audit.
2. Process and organization check
- Map internal processes relating to VAT (invoicing, accounting entries, regulatory follow-up).
- Update accounting procedure documentation.
- Regularly train key staff on new obligations (e.g., cross-border services, VAT threshold, deduction rights).
3. Managing the FTA audit
- Prepare to welcome auditors: ensure team and documentation are ready.
- Respond quickly to any requests for additional information.
- Anticipate typical questions: non-compliant invoices, subsidies/ancillary income, intra-group services.
4. Closure and follow-up of recommendations
- Immediately implement required recommendations or corrections.
- Document corrective actions for future audits.
Common errors found in SME audits
- Incorrect application of the reduced rate on ineligible services.
- Poor VAT management on expense claims or business gifts.
- Failure to allocate deductions on mixed expenses (personal/professional use).
- Omission to pay VAT on imported services (reverse charge mechanism).
Practical solutions to reinforce VAT compliance
- Outsource the VAT review to a fiduciary: ensures separation of duties, more objectivity and sector benchmarking.
- Digitize document management: implement an ERP that facilitates storage and lookup of supporting documents.
- Schedule regular internal audits, even when not required by law.
What is the role of a Geneva fiduciary in audit success?
Ark Fiduciaire supports Geneva SMEs with:
- Initial risk analysis (VAT compliance assessment)
- Assistance during the FTA audit (on-site presence, reasoned responses)
- Training internal teams on best practices
- Implementing digital archiving and tools (Odoo, third-party integrations)
- Post-audit follow-up (communications with FTA, corrective action plans)
What are the risks for SMEs in case of non-compliance?
- Retroactive tax adjustments (with interest) over multiple years
- Administrative penalties (fines)
- Reputational damage and blocked VAT refunds
Conclusion and practical advice from Ark Fiduciaire
Anticipating the VAT compliance audit is now a key lever for safety and tax optimization for any SME. Ark Fiduciaire provides structured, tailor-made support adapted to the Geneva context in 2025: audit preparation, internal control reviews, organizational advice and ongoing compliance monitoring.
For more information about our services tailored to your sector and structure, contact our experts.
Official references and useful links: