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Top Invoicing Software for Switzerland with Multi-Rate VAT Support

Easily create invoices with multiple VAT rates on the same invoice with these recommended invoicing softwares

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Finding software that handles multiple VAT rates on a single invoice is essential for Swiss freelancers—yet surprisingly few tools do it well. Whether you're a gardener invoicing plants at 2.6% and services at 8.1%, a hotel billing accommodation at 3.8% alongside restaurant meals, or a retailer selling mixed products, your invoicing software must properly split VAT rates and generate compliant MWST reports. After comprehensive research into Swiss platforms, international tools, and open-source alternatives, five solutions stand out as genuinely capable—and one surprising free option may be all most freelancers need.

This guide examines the full Swiss invoicing landscape, explains why multi-VAT support matters, and delivers actionable recommendations based on real capabilities rather than marketing claims.

Why multi-VAT invoicing is non-negotiable in Switzerland

Switzerland's VAT system operates with three active rates that frequently appear on the same invoice. Since January 1, 2024, these rates are:

8.1% standard rate (Normalsatz)

Most services, goods, and professional work

2.6% reduced rate (reduzierter Satz):

Food products, plants, books, medications

3.8% special rate (Sondersatz):

Hotel accommodation and overnight stays

0% exempt:

Healthcare, education, exports, certain financial services

The complexity emerges when a single transaction naturally spans multiple categories. A landscaper purchasing plants (2.6%) and providing installation services (8.1%) must split the invoice correctly. A hotel billing room nights (3.8%), restaurant dinner (8.1%), and minibar drinks (8.1%) needs three separate VAT calculations on one document.

Quarterly MWST declarations require precise breakdowns by rate. The Federal Tax Administration (ESTV) expects revenue reported separately for each VAT percentage. Software that merely tracks total VAT—without separating by rate—creates manual reconciliation nightmares every quarter.

Businesses that regularly need multi-VAT invoices

Garden centers and nurseries routinely invoice living plants at 2.6% alongside pots, tools, and decorations at 8.1%. Restaurants face constant split-rate scenarios: eat-in meals at 8.1%, takeaway at 2.6%, and alcohol always at 8.1% regardless of context. Retail shops mixing food products with household goods, pharmacies selling medications alongside cosmetics, and bookstores combining books with stationery all encounter this daily.

The 2024 rate increase from 7.7% to 8.1% (standard) and 2.5% to 2.6% (reduced) added another layer: software must handle historical invoices at old rates while applying new rates going forward. This rate-change capability separates professional tools from basic invoicing apps.

Swiss-native platforms lead for compliance and multi-VAT handling

After evaluating major Swiss invoicing and accounting platforms, clear patterns emerge. All established Swiss tools support MWST at a basic level—this is table stakes for the Swiss market. However, the quality of multi-VAT implementation per invoice varies significantly.

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Magic Heidi:
Purpose-built for Swiss freelancers

Magic Heidi represents the new generation of Swiss invoicing software, designed from the ground up specifically for Swiss freelancers and Einzelunternehmen. Based in Lausanne and founded in 2022, the platform takes a modern approach with AI-powered expense scanning that automatically extracts data from receipts and categorizes transactions. Multi-VAT invoicing is fully supported, allowing freelancers to bill plants at 2.6% and gardening services at 8.1% on the same invoice without manual calculations.

The platform generates compliant Swiss QR-bills automatically and handles MWST reporting with proper breakdowns by VAT rate for quarterly declarations. The modern, intuitive interface contrasts sharply with legacy Swiss accounting software, making it accessible to freelancers without accounting backgrounds. German, French, and English language support covers the major Swiss business languages.

✨Pricing runs CHF 30/month or CHF 299/year after a limited free trial, positioning it competitively against bexio while offering a more focused feature set tailored to solo operators rather than growing teams.

✨Key strength: The Swiss-specific focus means no configuration gymnastics—VAT rates, QR-bills, and MWST workflows work correctly from day one without adapting international software to local requirements.

✨Best for: Swiss freelancers wanting modern, mobile-friendly software purpose-built for their needs, those who value intuitive design over legacy feature depth, and anyone frustrated by clunky interfaces in traditional Swiss accounting tools.

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bexio:
Market leader with solid multi-VAT capabilities

bexio dominates the Swiss market with over 90,000 customers and represents the default choice for growing businesses. Its web application fully supports invoices with multiple VAT rates per line item, automatically calculating totals for each rate category.

The platform generates VAT reports compliant with Federal Tax Administration requirements, supporting both the effective method and net tax rate (Saldosteuersatz) approach. Banking integration with 70+ Swiss banks including UBS, ZKB, and PostFinance enables automatic reconciliation. QR-bill generation is fully integrated.

✨Pricing starts at CHF 35-45/month for the Starter plan (single user), reaching CHF 99-125/month for Pro+ with 25 users. Annual subscriptions save approximately CHF 120. This positions bexio as an investment rather than a budget option—appropriate for freelancers earning consistent revenue who value comprehensive features.

✨Key limitation: The bexio Go mobile app cannot handle multiple VAT rates on supplier invoices, forcing desktop use for complex scenarios. Some users report the interface feels dated despite functional depth.

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Crésus:
Best-documented multi-VAT implementation

Crésus from Epsitec has served Swiss businesses for over 30 years and dominates French-speaking Switzerland (Romandie). For multi-VAT workflows specifically, Crésus has the most explicitly documented capability among all platforms tested.

The documentation clearly explains entering each article on separate lines with different VAT rates in the same invoice, including period specification for invoices spanning rate changes. This attention to real-world complexity—acknowledging that a January invoice might include December work at old rates—demonstrates deep Swiss market understanding.

Crésus generates XML files for direct upload to the FTA portal (e-TVA/e-MWST), supports up to 25 different flat rates for the Saldosteuersatz method, and handles both agreed and received remuneration methods.

✨Pricing from CHF 20/month (subscription) or available as one-time purchase licenses makes it highly competitive. The modular approach (Comptabilité, Facturation, Salaires) lets freelancers pay only for needed functionality.

✨Best for: French-speaking freelancers, anyone needing explicit multi-VAT support with period handling, businesses working with fiduciaries familiar with the Crésus ecosystem.

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Banana Accounting:
Exceptional value with full VAT control

Banana Accounting from Lugano offers remarkable value for freelancers comfortable with spreadsheet-style interfaces. At CHF 89/year for Professional (turnover under CHF 100,000) or CHF 129/year for Advanced, it costs less than two months of most competitors.

Multi-VAT support operates through a comprehensive VAT codes system. Each transaction receives a code corresponding to its VAT rate, and the software calculates and separates everything automatically. The Advanced plan exports XML files formatted for direct FTA submission—a genuine time-saver during quarterly declarations.
The Excel-like interface appeals to users who think in spreadsheets. All Swiss VAT rates (8.1%, 2.6%, 3.8%, 0%) come pre-configured, and templates exist for various business types including canton-specific options.

✨Trade-off: Banana requires understanding double-entry bookkeeping fundamentals. It's not "set and forget" software—users must assign correct VAT codes deliberately. For freelancers with accounting knowledge or willingness to learn, this control becomes an advantage.

✨Best for: Budget-conscious freelancers, Italian-speaking users (Ticino), anyone preferring desktop software over cloud subscriptions, users who want data stored locally rather than in the cloud.

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CashCtrl:
The hidden gem with a genuinely free tier

CashCtrl from Basel represents perhaps the most underappreciated option in the Swiss market. Its permanently free tier includes full financial accounting, debtor/creditor management, and complete VAT handling—with no artificial transaction limits.

The platform supports automatic VAT booking with comprehensive tax reports, handles both effective and Saldosteuersatz methods, and generates reports formatted for Swiss MWST declarations. QR-bill support is fully integrated.
100% Swiss-hosted with Swiss development and support, CashCtrl addresses data sovereignty concerns directly. A full REST API enables custom integrations for technically-inclined users.

The Pro version at CHF 350/year adds multi-currency support, advanced reports, and API access. But the free tier alone meets most freelancer needs—genuinely meeting professional requirements without payment.

✨Best for: Freelancers starting out, anyone wanting full Swiss compliance without subscription costs, developers and technical users who value API access, privacy-conscious users wanting Swiss data hosting.

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Invoice Ninja:
Best international option with Swiss QR-bill support

Among international tools, Invoice Ninja uniquely supports Swiss QR-bills—the payment standard mandatory since October 2022. This open-source platform allows up to three separate tax rates per line item, enabling proper Swiss multi-VAT invoicing.

The free self-hosted version provides full functionality for technically capable users. Hosted plans start at approximately CHF 9/month, with Swiss hosting available through partners like Infiniroot for data sovereignty.

✨Critical limitation: VAT reports don't match Swiss MWST format out of the box. Freelancers must manually compile figures for quarterly declarations. No Swiss bank feed integrations exist. The platform works for invoicing but requires separate bookkeeping for full compliance.

✨Best for: Tech-savvy freelancers comfortable with self-hosting, businesses wanting open-source flexibility, users who can adapt international tools to Swiss requirements.

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International tools largely fail Swiss compliance requirements

The research reveals a consistent pattern: major international invoicing platforms lack critical Swiss features, making them poor choices for VAT-registered freelancers.

QuickBooks, FreshBooks, and Wave: Not suited for Switzerland

QuickBooks Online explicitly states it cannot generate Swiss VAT forms online. More critically, major Swiss banks including PostFinance aren't supported—a dealbreaker given PostFinance's prevalence among Swiss small businesses. No QR-bill support exists without third-party workarounds.

FreshBooks and Wave similarly lack QR-bill generation, Swiss bank integrations, and MWST-formatted reporting. While both support multiple tax rates per invoice technically, the missing Swiss-specific features create more work than they save.

Zoho and Xero: Partial adaptation possible

Xero comes closest to Swiss compatibility among major international platforms. It supports CHF, offers QR-bill generation, and connects to some Swiss banks. VAT reporting includes breakdowns by rate, though formatting for MWST declarations requires adaptation.

Zoho Books can be configured with Swiss VAT rates but lacks QR-bill support and native CHF handling. Both platforms suffer from English-focused support with limited German, French, or Italian assistance.

The verdict: international tools require significant manual effort for Swiss compliance. Unless specific circumstances mandate them (existing corporate standards, international operations), Swiss-native solutions provide better value.

Emerging Swiss platforms worth watching

Several newer Swiss tools target freelancers specifically with modern interfaces and competitive pricing.

Magic Heidi (Zurich, founded 2022) offers AI-powered expense scanning and mobile-first design specifically for Swiss freelancers. Multi-VAT support and QR-bill generation come standard. Pricing runs CHF 30/month or CHF 299/year after a limited free tier.

Milkee achieves the highest Google Maps rating (5/5 stars) among Swiss accounting apps. Built by a solo developer for German-speaking Einzelunternehmen, it emphasizes simplicity through the traditional "Milchbüchlein" approach. Pricing scales with turnover: CHF 19.90/month under CHF 30K, CHF 29.90/month above.

Swiss21/AbaNinja (backed by Abacus) provides a genuinely free tier including VAT handling and 70+ bank connections. The connection to Abacus's enterprise heritage means proven underlying technology, though the free tier has volume limitations.

Infinity Finance offers a modern, Stripe-inspired interface with AI-powered bank transaction categorization. Full MWST-Abrechnung capability costs CHF 25-40/month depending on team size.

Open-source options require Swiss configuration

For technically capable freelancers, open-source invoicing platforms offer flexibility and cost savings—but none provide Swiss compliance out of the box.

Invoice Ninja (discussed above) represents the best balance of features and configurability.

Dolibarr includes a specific "VAT Statement Module for Switzerland" available through DoliStore, though some VAT calculation bugs have been reported in recent versions.

InvoicePlane and Crater/InvoiceShelf support configurable tax rates but lack Swiss-specific features entirely. Users must manually configure VAT rates, create their own QR-bill solutions (or skip them), and compile MWST reports manually.

Key insight: No open-source tool natively generates Swiss QR-bills. This mandatory payment standard since 2022 represents a significant gap. Self-hosting also introduces responsibility for data backup, security, and uptime—acceptable for some freelancers, problematic for others.

The top 6 recommendations for Swiss freelancers

Based on comprehensive analysis of multi-VAT capabilities, MWST compliance, pricing, and ease of use, these five solutions genuinely serve Swiss freelancers with split-VAT invoicing needs.

❶ . Magic Heidi — Best purpose-built solution for Swiss freelancers

Designed specifically for Swiss freelancers from day one, Magic Heidi combines modern mobile-first design with proper multi-VAT invoicing, automatic QR-bill generation, and compliant MWST reporting. AI-powered expense scanning and an intuitive interface eliminate the learning curve of legacy Swiss accounting software. Recommended for: Swiss freelancers wanting software built specifically for their needs, those who value modern UX over feature bloat, mobile-first users who manage invoicing on the go.

❷ . CashCtrl — Best free option with full compliance

The free tier alone handles multi-VAT invoicing, MWST reporting, and QR-bills without artificial limits. Swiss-hosted, Swiss-developed, and fully capable. Recommended for: freelancers wanting professional tools without subscription costs, new businesses testing the market, anyone prioritizing Swiss data sovereignty.

❸ . Crésus — Best for complex multi-VAT scenarios

Explicitly documented support for mixed-rate invoices with period handling makes Crésus ideal for businesses regularly facing multi-VAT complexity. The 30-year Swiss market presence means proven compliance. Recommended for: French-speaking freelancers, businesses with complex VAT scenarios, those working with Crésus-familiar fiduciaries.

❹ . bexio — Best comprehensive platform for growth

Market-leading position means broad ecosystem support, extensive banking integrations, and comprehensive features beyond invoicing. Higher pricing reflects business-ready capabilities. Recommended for: freelancers planning to grow, those needing payroll integration, businesses wanting market-standard tools.

❺ . Banana Accounting — Best value for knowledgeable users

At CHF 89-129/year with full Swiss VAT support including FTA XML export, Banana offers exceptional value for users comfortable with spreadsheet-style interfaces. Recommended for: budget-conscious freelancers, those with accounting knowledge, users preferring desktop/offline software.

❻ . Invoice Ninja — Best for technical freelancers

The only international platform with Swiss QR-bill support, Invoice Ninja works well for tech-capable users who can configure Swiss VAT rates and compile MWST reports manually. Open-source option eliminates costs entirely for self-hosters. Recommended for: developers and technical freelancers, those comfortable without hand-holding, businesses needing international flexibility.

Making the final choice

A decision framework

Select CashCtrl if cost matters most and you want proven Swiss compliance without payment. Choose Crésus if you operate in French-speaking Switzerland or face complex multi-VAT scenarios regularly. Opt for bexio if you're willing to pay for market-leading comprehensiveness and growth potential. Pick Banana Accounting if you have accounting knowledge and want maximum value. Consider Invoice Ninja only if you're technically capable and need open-source flexibility, or pick Magic Heidi if you want something simple that does the job.

For most Swiss freelancers encountering multi-VAT invoicing occasionally, CashCtrl's free tier provides everything needed—making the common advice to pay CHF 35+/month unnecessary. For those invoicing complex VAT scenarios daily, Crésus justifies its modest subscription through explicit support for real-world complexity.

Essential Swiss VAT compliance checklist

Whatever software you choose, ensure it handles these Swiss requirements:

  • Multiple VAT rates per invoice with automatic calculation by rate
  • QR-bill generation (mandatory since October 2022)
  • MWST report generation breaking down revenue by VAT rate for quarterly declarations
  • 2024 rate support (8.1%, 2.6%, 3.8%) with historical rate handling
  • CHF as native currency with proper formatting
  • 10-year record retention capability for Swiss compliance

The 2024 VAT rate increase from 7.7% to 8.1% (standard) demonstrated the importance of software updates. Ensure your chosen platform actively maintains Swiss compliance as regulations evolve.

Conclusion

Swiss freelancers needing multi-VAT invoicing have strong options across price points. Magic Heidi emerges as the standout value, offering simple and Swiss-compliant invoicing. Crésus provides the most explicit multi-VAT documentation, ideal for complex scenarios. bexio remains the safe market-leader choice for those prioritizing ecosystem and growth potential. Banana Accounting delivers exceptional value for knowledgeable users, while Invoice Ninja serves technical freelancers wanting open-source flexibility

International tools like QuickBooks, FreshBooks, and Wave should generally be avoided—their missing QR-bill support and Swiss bank integrations create more problems than they solve. The Swiss invoicing software market has matured sufficiently that domestic options outperform adapted international alternatives for local compliance needs.