Best Invoicing Software for Czech Freelancers: An Honest Comparison

Short answer: for most Czech freelancers paid by bank transfer, Fakturoid is the safest default. iDoklad suits small teams, Vyfakturuj is the cheapest start for a new business, SuperFaktura has the cheapest paid plan with payment matching, and POHODA or Money S3 make sense if you want full desktop tax records or your accountant already uses them. There is no single best tool, only the best fit for how you get paid, whether you pay VAT and who does your books.

Disclosure: I build MoneySky, one of the tools below. It gets the same treatment as the others, weaknesses included.

How to choose: six questions that matter

1. What does it cost at your size?

Most free plans are capped at around five clients or contacts, so they work for a side project, not a full-time business. Check what the plan you will actually need costs, not the entry tier: payment matching and VAT outputs often sit one or two tiers higher. Annual billing and new-business discounts can cut the first year a lot.

2. Are you paid by bank transfer or in person?

EET 2.0 starts on 1 January 2027 (January is a trial period, full operation from 1 February 2027). It covers payments taken in personal contact with the customer: cash, card, QR code and vouchers. Remote bank transfers, payment gateways and e-shop QR payments are outside it. A freelancer who invoices and gets paid by transfer is mostly unaffected. If you take card or cash in person, you need a tool that supports EET 2.0, or the free state app MOJE EET, expected from 1 December 2026.

3. Are you a VAT payer, and do you have EU clients?

Non-payers mostly care about the income tax return and the social and health insurance přehledy. VAT payers need the VAT return, kontrolní hlášení and, with EU business clients, souhrnné hlášení. Selling to EU consumers adds OSS. Keep an eye on the VAT registration threshold too. Most tools here export ISDOC, the Czech e-invoice format. Peppol matters if you invoice Slovak clients, because Slovakia makes Peppol e-invoicing mandatory from 1 January 2027.

4. What software does your accountant use?

If your accountant runs POHODA or Money S3, a tool that exports cleanly to it (or comes from the same vendor) saves them time and you money.

5. Does it match payments with your bank?

Most Czech invoicing apps match payments through bank e-mail notifications, and the list of supported banks differs. If you bank with mBank, check carefully: Fakturoid and iDoklad do not support it.

6. What happens when you grow?

More users, a second company, or a move to an s.r.o. with double-entry bookkeeping. Look at per-user pricing and whether you can run several companies in one account. If an s.r.o. might make sense for you, check exports to full accounting software.

Summary table

Prices excluding VAT as listed on the providers' websites in October 2026 (Vyfakturuj does not state the VAT basis of its headline prices; MoneySky is priced in EUR). Check their pricing pages before you decide.

The tools one by one

Fakturoid

The most polished Czech invoicing app, on the market since 2009. From Na lehko (164 Kč a month) you get the income tax return with the ČSSZ přehled, a running estimate of social and health contributions, and paušální daň and VAT threshold monitoring. Payment matching starts on Na každý den (231 Kč) and supports most Czech banks plus the Fio API. The free MCP server, the API on every plan and exports to seven accounting programs make it the developer's choice. EET 2.0 support is announced for all paid plans, not yet live. New businesses (IČO under 12 months) get 50% off the first annual invoice.

Weaknesses: the VAT return, kontrolní hlášení, souhrnné hlášení and OSS are on Na maximum only (429 Kč). Extra users cost extra. No mBank. Quotes are top plan only.

Best for: solo freelancers paid by transfer, and anyone who wants to automate. See the Fakturoid pricing.

iDoklad

Made by Seyfor, the company behind Money S3. Users are included (2, 5 or 9 by plan), and Oblíbený (358 Kč a month on annual billing) brings payment matching, prodejky, the VAT return, kontrolní hlášení and income tax supporting data. It integrates with Money S3, S4, S5, Pohoda and Vario from Základní. AI Inbox extracts received documents. The 60-day trial needs no card.

Weaknesses: matching and tax outputs only from Oblíbený. No new-business discount, no Peppol mention, no EET 2.0 announcement found as of October 2026, no MCP server.

Best for: small teams and businesses whose accountant uses Money. See the iDoklad pricing.

Vyfakturuj

Plans are listed at 175 Kč (Mini), 299 Kč (Ideal) and 620 Kč a month for three companies (Profi); the page suggests these are annual-billing prices excluding VAT but does not say so plainly. The standout is the new-business discount: 80% off the first annual subscription if your IČO is younger than 24 months. Matching starts on Mini, and from Ideal you can take card payments through GoPay, Stripe, PayPal, Comgate and others. It exports to Pohoda, Money S3 and DUEL and prepares partly pre-filled VAT data for MOJE daně.

Weaknesses: no mention of income tax, přehledy or Peppol, no EET 2.0 announcement found. The Fio API is Profi only.

Best for: new businesses in their first two years, and anyone who wants clients to pay invoices by card online.

SuperFaktura

The cheapest paid plan with payment matching: Základní at 129 Kč a month excluding VAT. Half-yearly and yearly billing are offered, but the page does not spell out the yearly price. Its bank list includes mBank, Revolut and Equa, which most competitors lack, though the matching method varies by bank. The VAT return, kontrolní hlášení and souhrnné hlášení start on Standardní (279 Kč). The Slovak version says it can send and receive invoices over Peppol.

Weaknesses: one user plus an accountant until Prémiový (469 Kč), API only on Prémiový, no income tax or přehledy mentioned, no EET 2.0 announcement found, no Peppol mention on the Czech version.

Best for: a tight budget, mBank or Revolut users, and businesses with a Slovak side. See the SuperFaktura pricing.

mPOHODA and POHODA Mini

mPOHODA is Stormware's cloud invoicing app. Start is free within limits (5 contacts, 100 issued invoices), Basic costs 199 Kč a month or 1,990 Kč a year, and Pro adds 5 users and the API. Bank connection works with any bank via Everifin, plus direct Fio. POHODA Mini is the desktop option: a 2,980 Kč licence plus 980 Kč a year for updates, covering daňová evidence, invoicing, the VAT return, souhrnné hlášení and income tax supporting data. Stormware has confirmed EET 2.0 support for all POHODA variants, with a free mKasa app.

Weaknesses: POHODA Mini lacks homebanking, foreign currencies and assets. The desktop route is heavier than a web app. See the mPOHODA pricing.

Best for: anyone whose accountant uses Pohoda, and people taking payments in person who want confirmed EET 2.0 support.

Money S3 Basic

Desktop software for daňová evidence: a 2,990 Kč licence plus 1,690 Kč a year for updates (free in the year of purchase). It has the broadest tax coverage in this list: VAT return including OSS, kontrolní hlášení, souhrnné hlášení, the income tax return and both přehledy, with electronic submission. Homebanking, assets and kniha jízd are included.

Weaknesses: paušální daň is not mentioned, cloud access costs 950 Kč per user a month, and no EET 2.0, Peppol or AI announcements were found. It is a bookkeeping program first, so invoicing is less pleasant than in the web apps.

Best for: freelancers claiming actual expenses who want every form in one program.

MoneySky

A web app that combines invoicing with bank sync across all your accounts, business and personal. It connects to 2,686+ banks in the EU, EEA and UK through PSD2 open banking (including mBank), matches invoice payments automatically, and downloads every invoice as ISDOC and Peppol UBL. On the tax side it compares flat-rate expenses, actual expenses and paušální daň, and prepares the VAT return, income tax return and přehledy. One account can run an OSVČ and an s.r.o. at no extra cost. One plan at €7.99 a month or €79.90 a year (roughly 200 Kč a month).

Weaknesses: no free plan, no quotes or prodejky, no team seats, no native mobile apps (it installs on your phone as a web app), no client payment portal or card payment link, no Peppol network sending, no EET 2.0 support for in-person payments. It is younger, with a smaller user base, and not double-entry software.

Best for: freelancers who mix personal and business money and want invoicing, banks and Czech taxes in one place.

Quick picks

• Solo freelancer paid by transfer: Fakturoid.

• New business: Vyfakturuj (80% off the first year, IČO under 24 months) or Fakturoid (50%, under 12 months).

• Small team: iDoklad.

• Accountant uses Money S3: iDoklad, or Money S3 Basic if you want the books yourself.

• Accountant uses Pohoda: mPOHODA or POHODA Mini.

• In-person card or cash payments: POHODA (EET 2.0 confirmed) or Fakturoid (announced).

• Tight budget with payment matching: SuperFaktura.

• Developer who wants automation: Fakturoid.

• Invoices, all bank accounts and tax planning together: MoneySky.

• Moving to double-entry bookkeeping: your accountant's program; ABRA Flexi Basic includes double-entry and is listed at 390 to 425 Kč per user a month.

FAQ

Is there a free invoicing app for OSVČ?

Yes. Fakturoid, iDoklad, Vyfakturuj, SuperFaktura and mPOHODA all have free plans, typically capped at about five clients or contacts. They are fine for occasional invoicing. Payment matching and tax outputs need a paid plan.

Do I need accounting software as OSVČ?

Not necessarily. With flat-rate expenses or paušální daň, an invoicing app that tracks your income is usually enough. If you claim actual expenses, you need full tax records (daňová evidence), which POHODA, Money S3 or a good invoicing app with expense tracking can cover. Double-entry accounting is mainly for companies.

Which invoicing app supports EET 2.0?

As of October 2026, Stormware has confirmed EET 2.0 for all POHODA variants, Fakturoid has announced it for all paid plans (not live yet) and ABRA Flexi says it is in preparation. I found no announcement from iDoklad, Vyfakturuj, SuperFaktura or Money S3. If clients only pay by bank transfer, EET 2.0 mostly does not apply to you.

What is ISDOC?

ISDOC is the Czech standard for electronic invoices: an XML format, often embedded in the PDF, that your client's accounting software can import without retyping. Fakturoid, Vyfakturuj, SuperFaktura, POHODA and MoneySky export it, and iDoklad reads incoming ISDOC documents automatically.

Use the freelancer tax calculator to see what your invoices leave you after tax. If MoneySky sounds like a fit, you can try it free for 14 days, no card required.