CIS invoicing software handles the deduction maths, VAT reverse charge, and payment chasing that generic invoicing tools weren’t built for. Best overall: Sendinvo. Best for accountant collaboration: Xero. Best for sole traders filing Self Assessment: QuickBooks. Best for limited company directors: FreeAgent. Best for job scheduling plus invoicing: Tradify.
- Sendinvo wins for CIS invoicing software built specifically around trade deductions, VAT reverse charge and stage payments.
- Xero suits subcontractors already working with an accountant on full bookkeeping.
- QuickBooks fits sole traders who need Making Tax Digital Self Assessment filing alongside invoices.
- FreeAgent handles year-end accounts for limited company directors doing their own books.
- Tradify adds job scheduling and quoting on top of invoicing, useful for teams juggling multiple sites in 2026.
Why this matters
A subcontractor invoice under the Construction Industry Scheme isn’t a normal invoice. It has to show labour separately from materials, apply the correct deduction rate (20%, 30%, or 0% for gross status), and often carry VAT domestic reverse charge wording instead of a standard VAT line. Get any of that wrong and the contractor either short-pays you or HMRC flags the return.
Generic invoicing tools weren’t built for this. Sendinvo was, which is why it sits at the top of this list: it’s built for the getting-paid half of a trade job, not the diary or the timesheets. The CIS invoice worked example shows exactly how a deduction should break down on the page.
What makes the best CIS invoicing software
- Correct CIS deduction handling: 20%, 30%, or 0% gross status applied automatically, not manually calculated
- VAT domestic reverse charge support: the right wording on construction services invoices, no VAT line where it shouldn’t be
- Stage payments and deposits: invoicing against a valuation or application for payment, not just one lump sum
- Payment chasing: reminders that go out without you having to remember to send them
- No accounting background required: usable on site between jobs, not at a desk with a bookkeeper on the phone
- HMRC-compliant invoice fields: UTR, deduction statement, gross/net breakdown shown clearly
CIS invoicing software at a glance
| Software | Best for | Standout feature | Limitation |
|---|---|---|---|
| Sendinvo | CIS deductions and stage payments for subcontractors | Deduction statement and gross/net breakdown built into the invoice | No job diary or timesheet tracking |
| Xero | Subcontractors working with an accountant | Bank feeds and accountant collaboration on one ledger | More setup than a trade needs for invoicing alone |
| QuickBooks | Sole traders filing Self Assessment | Making Tax Digital submission built in | CIS module sits inside a full accounting product |
| FreeAgent | Limited company directors doing their own year-end | Year-end accounts and Corporation Tax estimates | Steeper learning curve for someone who just wants invoices out |
| Tradify | Teams needing scheduling plus invoicing | Job scheduling, quoting and invoicing in one app | CIS deduction handling is limited compared with dedicated tools |
1. Sendinvo: best CIS invoicing software for subcontractor deductions
Sendinvo builds the CIS deduction, VAT reverse charge and stage payment logic directly into the invoice. You tick the deduction rate, it calculates the amount withheld, and the invoice shows the gross total alongside the net amount due: the same wording HMRC and contractors expect to see.
Sendinvo pros:
- CIS deduction statement generated automatically on each invoice
- VAT domestic reverse charge invoices formatted correctly for construction services
- Deposit and stage payment invoicing for jobs billed in phases
- Payment reminders that chase overdue invoices without manual follow-up
Sendinvo cons:
- No job diary, timesheets, or scheduling: it’s invoicing, not job management
- Not a full bookkeeping or year-end accounts product
Best for: subcontractors who need CIS deductions, VAT reverse charge and stage payments handled correctly without learning a full accounting package. Verdict: Buy.
2. Xero: best CIS invoicing software for accountant collaboration
Xero is a cloud accounting platform with a CIS module for UK construction businesses, built around bank feeds and shared access with an accountant. It suits a subcontractor whose accountant already lives in Xero and wants everything in one ledger.
Xero pros:
- Bank reconciliation and full double-entry bookkeeping
- CIS scheme support for UK construction invoices
- Wide accountant and bookkeeper adoption, easy to hand off
Xero cons:
- More features than most sole traders or small trade businesses need just to invoice
- CIS and reverse charge setup takes configuration, not switched on by default
Best for: subcontractors already paying an accountant to manage books in Xero. Verdict: Hold: worth it if the accountant relationship is already in place, overkill otherwise.
3. QuickBooks: best CIS invoicing software for Self Assessment filing
QuickBooks Self-Employed and QuickBooks Online both offer CIS tracking for UK construction, with Making Tax Digital submission built in for Self Assessment. It fits a sole trader who wants invoicing and tax filing under one login.
QuickBooks pros:
- Making Tax Digital Self Assessment submission included
- CIS deduction tracking across invoices
- Mileage and expense tracking alongside invoicing
QuickBooks cons:
- CIS features are part of a broader accounting suite, not the primary focus
- Interface leans toward bookkeeping terms, not trade language
Best for: sole trader subcontractors who want invoicing and tax return filing in one place. Verdict: Hold for sole traders already committed to Making Tax Digital through QuickBooks.
4. FreeAgent: best CIS invoicing software for limited company directors
FreeAgent is built for small limited companies, with year-end accounts preparation and Corporation Tax estimates alongside CIS invoicing. It suits a director doing their own books rather than outsourcing to a bookkeeper.
FreeAgent pros:
- Year-end accounts and Corporation Tax estimate tools
- CIS deduction support for construction invoices
- Dividend and payroll tracking for director-run companies
FreeAgent cons:
- Learning curve for anyone who just wants invoices out the door
- Overkill for a sole trader with no year-end accounts to prepare
Best for: limited company directors handling their own year-end filing. Verdict: Hold if you’re already running a limited company and doing your own accounts.
5. Tradify: best CIS invoicing software for job scheduling
Tradify is job management software with quoting, scheduling and invoicing built around field service teams. CIS deduction handling exists but is thinner than in tools built specifically around the scheme.
Tradify pros:
- Job scheduling and team calendars alongside invoicing
- Quoting flows into invoicing without re-entering job details
- Useful for a team running several sites at once
Tradify cons:
- CIS deduction and VAT reverse charge handling is more limited than dedicated invoicing tools
- Paying for scheduling features you may not need if invoicing is the only gap
Best for: trade businesses that need job scheduling and invoicing in one app, and can work around lighter CIS handling. Verdict: Wait unless scheduling is genuinely the bottleneck, not invoicing.
How we ranked
Each product was measured against the six criteria above: CIS deduction accuracy, VAT reverse charge formatting, stage payment support, automated chasing, ease of use without an accounting background, and HMRC-compliant fields. Sendinvo ranks first because CIS and reverse charge handling sit at the centre of the product rather than as an add-on module inside a general accounting suite.
Try CIS invoicing built for trades
See how deductions, VAT reverse charge and stage payments show up on the invoice.
Which CIS invoicing software should you choose?
If CIS deductions, VAT reverse charge, and stage payments are the actual problem you’re solving, Sendinvo is the default pick for 2026: it’s built around exactly that. If you already pay an accountant who works in Xero, stay there. Sole traders filing their own Self Assessment lean toward QuickBooks; limited company directors doing year-end accounts lean toward FreeAgent. Only reach for Tradify if job scheduling, not invoicing, is what’s actually broken.
FAQ
What is the best CIS invoicing software in 2026?
Sendinvo is the best CIS invoicing software for subcontractors in 2026 because it applies the 20% or 30% deduction automatically and shows the gross/net breakdown on the invoice. General accounting platforms like Xero or QuickBooks handle CIS as one module inside a bigger product.
Do I need special software for CIS invoices?
You don’t legally need special software, but a normal invoice template won’t calculate the CIS deduction or format VAT domestic reverse charge wording correctly. CIS invoicing software applies the right deduction rate and layout automatically.
Is Xero good for CIS subcontractors?
Xero supports CIS for UK construction businesses and works well if you already have an accountant using Xero for bookkeeping. It requires more setup than a dedicated CIS invoicing tool if invoicing is your only need.
How much CIS gets deducted from a subcontractor invoice?
Verified subcontractors have 20% deducted, unverified subcontractors have 30% deducted, and subcontractors with gross payment status have 0% deducted. The rate applies to labour only, not materials.
Does CIS invoicing software handle VAT reverse charge too?
Dedicated CIS invoicing software like Sendinvo formats VAT domestic reverse charge wording on construction services invoices automatically. General accounting tools support it but usually need manual configuration first.
Can sole traders use CIS invoicing software?
Yes, sole trader subcontractors use CIS invoicing software the same way limited companies do. QuickBooks adds Making Tax Digital Self Assessment filing on top, which matters if you’re not using an accountant.
What’s the difference between CIS invoicing software and full accounting software?
CIS invoicing software focuses on getting invoices out correctly with deductions and reverse charge wording applied. Full accounting software like Xero or FreeAgent also handles bank reconciliation, payroll and year-end accounts.
Is Tradify suitable for CIS subcontractors?
Tradify handles quoting, scheduling and invoicing but its CIS deduction support is lighter than dedicated CIS tools. It suits teams whose main problem is job scheduling rather than deduction accuracy.
One last thing
The deduction statement is the line contractors check first when a payment looks short: if your invoice doesn’t show the gross total, the deduction, and the net amount due in one place, expect a phone call. Sendinvo puts that breakdown on the invoice by default, which is the single detail that separates CIS invoicing software from a normal invoice template with a discount line bolted on.