Best Payroll Software for Swiss SMEs and Startups in 2025

Payroll is one of the most sensitive and complex areas of business administration in Switzerland. With numerous mandatory contributions (AHV, ALV, BVG, etc.), complex withholding tax rules, monthly declarations, and the need for year-end salary certificates, there’s a lot to handle—especially for startups and SMEs with limited internal resources.

Digital tools have emerged to simplify these tasks, reduce the risk of error, and help businesses stay compliant. But choosing the right software involves much more than simple feature comparisons. Implementation, configuration, and ongoing use all require the right expertise.

In this article, we look at the evolution and advantages of digital payroll systems, the most important features these tools offer, common pitfalls and risks when using payroll software, a comparison of leading tools used by Swiss startups and SMEs, and why having the right fiduciary partner matters just as much as the software itself.

How has payroll accounting changed in Switzerland?

Until the last decade, many Swiss SMEs still relied on manual processes or rigid desktop software to manage payroll. Wage calculations were done in spreadsheets, and monthly declarations involved time-consuming filling of forms and paper submissions. This meant a great deal of wasted time and effort.

2013 saw the introduction of Swissdec 4.0, a key milestone in the digitalization of payroll accounting in Switzerland. The new standard allowed for structured, electronic wage reporting (ELM) to authorities, which encouraged software providers and employers alike to shift to digital systems.

Today, payroll software has evolved into a critical part of the business toolkit. Digital solutions now offer secure, cloud-based access to real-time data, automate calculations and submissions, and integrate with accounting, time tracking, and HR systems. Many are certified by Swissdec (the latest version now being 5.0), meaning they support the official electronic wage reporting standard, which is becoming the default for compliance.

For startups and growing SMEs, digital payroll tools reduce administrative burden, improve legal compliance, and offer transparency for both employers and employees. But not all tools are created equal, and effective payroll still depends on correct setup, ongoing oversight, and expert handling.

What are the main advantages of digital payroll tools?

Some of the key benefits of payroll software for Swiss SMEs and startups include:

• Efficiency: Automated calculations and recurring processes save time each month.
• Compliance: Software is continuously updated to reflect current laws and contribution rates, reducing legal risk.
• Accuracy: Minimizes errors in wage statements, deductions, and year-end declarations.
• Integration: Links to existing accounting, ERP, and HR systems.
• Transparency: Employers and employees can access payroll data and documents anytime.
• Scalability: As a business grows, digital payroll can easily support more employees and more complex needs.
• Security: Payroll data is stored securely with encryption, controlled access, and reliable backups, reducing risk of data loss or breaches.
• Simplicity: Clear interfaces, automated workflows, and predefined wage types make it easier for non-experts to manage payroll.
• Reliability: Cloud platforms ensure consistent access, uptime, and performance, even across multiple locations or teams.
• Global payroll management: Some tools support multi-currency, multilingual payroll processes, making them suitable for international teams or cross-border employment.

What are the key features offered by modern payroll systems?

Digital payroll tools often come packed with features designed to make Swiss payroll more efficient, compliant, and user-friendly. But not every SME necessarily needs the full suite, and not every provider implements them equally well. Here are the key features to understand when comparing payroll solutions:

Automatic salary calculations

Most digital tools automatically calculate gross-to-net salary for each employee based on their personal data, role, contract, and location. This includes deductions for AHV/IV/EO, ALV, BVG, withholding tax (if applicable), and other mandatory contributions. The system applies current rates and thresholds based on Swiss law.

E-filing with authorities

Modern payroll systems can submit salary declarations electronically to AHV compensation offices, tax authorities, and accident insurance providers. This reduces paperwork, saves time, and ensures deadlines are met.

Multi-canton and multi-rate support

Some companies employ people across different cantons, or with varying church tax affiliations and municipal rates. Good software supports multiple cantonal configurations and ensures the correct deductions are applied.

Payslip generation and employee portals

Tools generate legally compliant payslips, including the mandatory annual salary certificate (Lohnausweis), and allow secure digital access for employees. Many systems offer employee portals where staff can retrieve their own documents, submit updates, or track leave balances.

Absence and time tracking integration

Some platforms include or integrate with attendance systems, letting employers link overtime, sick days, or vacation directly to payroll. This ensures precise, automated calculations for variable salaries.

Accounting system integration

Once salaries are processed, entries can be booked directly into the accounting system. This minimizes manual data transfer, reduces reconciliation errors, and speeds up monthly closing.

Automatic updates for legal changes

Payroll regulations change frequently—for example, withholding tax rates, AHV contributions, or minimum insured income thresholds for pensions. High-quality software updates these parameters automatically, so employers remain compliant.

Document archiving and audit trail

Digital payroll tools store documents securely and allow users to retrieve them for audits, inspections, or internal reporting. Many also log changes for a clear audit trail.

Multilingual functionality

Most Swiss payroll tools support German, French, Italian, and English; both in the interface and for generated documents like payslips. This is especially helpful for international teams or companies in multilingual regions.

Custom rules and special cases

The better tools can handle special cases like bonus payouts, benefits-in-kind, cross-border commuters, expense reimbursements, and maternity/paternity leave. They allow for rule-based configurations and one-off adjustments.

Features are great, but how effective are they in reality?

These features are widely available with most of the top digital payroll tools, but what matters most is how reliably and correctly they are applied. A tool that ticks all the boxes on paper isn’t necessarily the one that will work best in practice—especially without a knowledgeable partner handling the setup and ongoing use.

That’s why it’s important not just to ask what a tool can do, but how it will perform in your specific business setup. Who will manage it day-to-day? How quickly can issues be resolved? Will the tool stay up to date with regulatory changes? The answers to these questions often matter more than the features themselves.

That’s why it’s also vital to find the right payroll partner to take care of the practical implementation for you—someone who not only understands the technical setup but also knows how to tailor the tool to your specific needs, monitor changes, and ensure accuracy month after month. As a trusted fiduciary partner to SMEs and startups in Switzerland, Nexova provides exactly this type of essential support and more.  

What are the limitations and risks to watch out for?

Even the best payroll tool can lead to problems if used incorrectly. Some common pitfalls include:

• Incorrect setup: If employee profiles, insurance settings, or tax codes are entered incorrectly, the results will be wrong—even if the tool looks correct (GIGO – garbage in, garbage out)
• Overreliance on automation: Software can’t always interpret special cases or complex legal nuances. Blind trust in automated outputs can therefore lead to unnoticed errors, especially in non-standard employment situations.
• Lack of support: Some low-cost providers offer limited guidance, leaving SMEs to navigate compliance alone. Without proper onboarding or ongoing support, small issues can lead to costly mistakes.
• Incomplete coverage: Not all tools support cross-border scenarios or multi-canton employment. Missing features for local variations or unique cases can result in inaccuracies.

Ultimately, payroll software doesn’t replace the need for professional knowledge, it just enables those with the necessary expertise to handle your payroll more efficiently, accurately, and securely.

Which payroll tools are best for Swiss startups and SMEs in 2025?

Founded in 1998, SwissSalary 365 is one of the most advanced and reliable payroll solutions in the Swiss market, especially for SMEs that want scalable, cloud-based payroll integrated with their broader financial operations.

It is built on top of the Microsoft Dynamics 365 ecosystem, and therefore integrates seamlessly with Microsoft Dynamics 365 Business Central, along with other widely used ERP systems in Switzerland. This makes SwissSalary an ideal solution for companies already utilizing the potential of Dynamics 365, as well as all growing businesses and those with more complex payroll structures.

The platform was the first payroll provider in Switzerland to acquire the Swissdec certified plus label (Swissdec 5.0). It offers automatic updates for legal changes such as AHV/ALV rates and withholding tax, compliance with the latest collective labor agreements (GAV), and powerful reporting capabilities.

Payroll data is processed securely in the cloud, with real-time backups and compliance reporting available on demand. The system can also generate detailed reports and insights for HR or finance teams.

At Nexova, we use SwissSalary for our clients’ payroll processing because it integrates flawlessly with our workflows, supports full compliance, and handles everything from standard payroll to special cases with consistency and control. Best of all, outsourcing payroll accounting with SwissSalary allows businesses to benefit from enterprise-grade tools without needing to invest in complex setup, licenses, or in-house expertise.

Strengths: Fully cloud-based, automatic legal updates, strong integration with Microsoft Dynamics 365 Business Central, Swissdec 5.0 certified, granular reporting, strong scalability, ideal for SMEs that need expert-led payroll processes.

Limitations: Requires proper onboarding and configuration, better suited when used with fiduciary partners familiar with the system.

1.      Abacus

Abacus Payroll is one of Switzerland’s most established payroll solutions, used to process over 1.5 million payrolls each month. It’s part of the broader Abacus ERP suite and supports advanced features like concurrent employment, multilingual payrolls, flexible cost center allocation, and integration with HR and time tracking.

Fully Swissdec-certified and regularly updated, it’s ideal for SMEs with complex payroll needs and internal or fiduciary expertise to manage setup and configuration.

Strengths: Established and trusted ecosystem, supports advanced payroll needs, well-integrated with HR and ERP systems, Swissdec-certified, scalable for SMEs.

Limitations: Pricing and licensing can be complex, setup requires expertise, generally needs the support of a trustee for effective use.

2.      Bexio

Bexio is a user-friendly cloud solution built for Swiss SMEs, startups, and sole proprietors. It combines accounting, invoicing, and payroll in one platform, and allows trustees to collaborate easily with clients.

Payroll can be added to existing Bexio packages and includes essentials like automatic AHV/BVG deductions, payslip generation, and electronic wage reporting.

Strengths: Modern UI, simple to use, good integration with accounting and e-banking, transparent pricing, strong customer support included in the price.

Limitations: Limited scalability, not ideal for complex or multi-canton payroll setups, payroll module only available with broader Bexio suite.

3.      KLARA

KLARA Payroll is a Swissdec-certified payroll module available within the KLARA Accounting platform, designed specifically for Swiss SMEs. It automates wage calculations, ELM wage reporting, and salary payments, with a simple and intuitive interface that suits even users without prior accounting experience.

The service costs CHF 3.90 per payslip with a KLARA business package (or CHF 4.90 without) and integrates with KLARA’s broader business tools for accounting, order management, and expense tracking. Its widget-based structure and affordable pricing make it a practical option for small businesses with straightforward needs.

Strengths: Affordable and easy to use, good for SMEs with simple payroll setups, part of a broader accounting ecosystem, no fixed license costs.

Limitations: Limited customization and extension options, less suitable for companies with complex needs or many employees.

4.      Infoniqa (Formerly Sage)

Infoniqa’s payroll software builds on the former Sage product line, long established in Switzerland and rebranded under the Infoniqa name in 2022. The software offers a hybrid model, combining both desktop and cloud functionality, with flexible packages and price ranges to suit various needs and budgets.

The accounting package includes the main key features like payroll accounting, VAT handling, e-banking, and bank reconciliation. Its interface is clean and structured, with a dashboard that helps users prioritize tasks and automate routine processes. Infoniqa is modular and adaptable across industries, and now promotes strong integration with Microsoft Dynamics 365 Business Central with their Payroll 365 software for users seeking full digital HR workflows.

Strengths: Broad functionality, hybrid cloud/desktop model, modular structure, MS Dynamics 365 integration.

Limitations: Some interfaces feel dated, pricing can be complex, onboarding requires training depending on the package.

Why software alone isn’t enough

The payroll tools we have listed all come packed with powerful features for enhancing and simplifying payroll management, meeting all Swiss legal standards and supporting electronic wage reporting via Swissdec.

However, efficient and accurate payroll management doesn’t come simply by using the right tool—it comes from using it correctly, which is where expert support makes the difference.

Payroll software is only as good as the person or team utilizing it. That’s why many growing businesses choose to outsource payroll accounting to a fiduciary partner who can configure, monitor, and manage payroll systems on their behalf. This is especially true in situations involving:

• Withholding tax across cantons and for different nationalities
• International staff or contractors
• Expense reimbursements or benefits-in-kind
• Year-end salary certificates and corrections

At Nexova, we work with top-tier payroll tools like SwissSalary, but our main value lies in how we use them to best serve our clients. We review each case carefully, apply the right compliance checks, and ensure your payroll stands up to internal and external review.

How should you choose the right setup for your business?

There are a multitude of advanced payroll tools available in Switzerland, and it’s important to realize that there is no one tool that is the perfect fit for all businesses.

The best solution depends on your company’s size, internal resources, and operational complexity. However, there are a few core factors to consider when choosing the right payroll software setup for your business:

• Legal compliance: Ensure the tool handles all Swiss social insurance deductions (AHV, ALV, BVG, UVG, KTG etc.), withholding tax, and wage statements in line with current law. Ideally, legal changes should be updated automatically.
• Swissdec certification: Look for tools that are Swissdec 5.0 certified. This guarantees they support the standardized ELM wage reporting procedure and meet national compliance standards.
• Integration with other systems: A good payroll tool should integrate with your accounting software, time tracking tools, ERP and HR systems, and e-banking. This avoids data silos and manual reconciliations.
• Functionality and ease of use: Choose software that makes routine tasks—like payroll creation, sending payslips, updating employee data, or processing adjustments—simple and intuitive. Easy navigation is essential, especially for companies without a full HR and accounting team.
• Flexible costs and licensing: Compare the license models, support fees, and ongoing costs. SaaS models are common and often scalable, but initial setup, support, and training can vary significantly in price.
• Future scalability: As your business grows, your payroll needs may change. Look for software that allows for modular expansion, such as adding time tracking, expense management, or more detailed cost center accounting as these features become needed.
• Trustee collaboration: If you work with a fiduciary, it’s essential that your payroll software allows for shared access and easy collaboration. Your payroll works best when your accountant or payroll partner is familiar with your tool and can support you actively.

Ask yourself the following questions to help narrow your choice of the right payroll software and service model for your needs:

• Do you have internal payroll expertise?
• How many employees do you have? Across how many cantons?
• Do you need integration with your accounting or time-tracking tool?
• Are you dealing with cross-border employees?

If your setup is straightforward, a basic cloud tool may be enough. If it’s more complex, partnering with a payroll provider like Nexova can save time, reduce risk, and help you scale smoothly.