Dedicated CIS apps vs general expense tracking — an honest comparison for UK construction subcontractors.
CIS subcontractors have a specific tracking problem: you need to log job income, materials and travel expenses, and keep track of the 20% (or 30%) CIS deductions your contractor makes at source, since most subcontractors are owed a refund at year end. Here's how the main options compare as of August 2026.
| Tool | Type | CIS-specific features | Best for |
|---|---|---|---|
| CIS Tracker UK | Mobile app | Tracks CIS deductions, estimates refund, generates SA103/SA108 figures | Subcontractors wanting a dedicated CIS-first app |
| CISDesk | Free iPhone app | Logs jobs, generates Payment & Deduction Statements, MTD-ready summaries | iPhone users wanting a free, CIS-specific tracker |
| Coconut | Mobile-first accounting app | MTD-compliant expense tracking designed with subcontractors in mind | Subcontractors who also want broader expense/invoicing features |
| PayToolkit Expense Tracker + CIS Tax Refund Estimator | Free web tool | Logs income/expenses free, separate CIS Tax Refund Estimator calculates likely refund | Subcontractors wanting a free, no-signup way to track expenses and estimate their refund |
Dedicated CIS apps like CIS Tracker UK and CISDesk are built specifically around the Payment & Deduction Statement workflow, which is genuinely useful if CIS is your main income source. Coconut takes a broader accounting-app approach with CIS support built in. PayToolkit's combination of the free Expense Tracker and CIS Tax Refund Estimator covers the core need — tracking expenses and estimating your refund — without a subscription, though it doesn't generate official Payment & Deduction Statements the way a CIS-specific app does.
Whichever tool you use, the two things worth getting right are: keeping a genuine running record of allowable expenses (materials, tools, travel between sites, protective equipment) rather than reconstructing them in January, and understanding that your CIS deductions are effectively advance tax payments — most subcontractors with genuine expenses are owed money back, but only if the expenses are properly claimed on your Self Assessment return.
We're not affiliated with CIS Tracker UK, CISDesk or Coconut. Pricing and features checked August 2026 and may have changed — always confirm current details directly with the provider.
A general expense tracker covers the core need of logging income and expenses — CIS-specific apps add extras like generating official Payment & Deduction Statements, which matters more if you deal with multiple contractors.
It depends entirely on your allowable expenses and other income — the CIS Tax Refund Estimator gives a quick estimate based on your specific figures.
No — CIS deductions (20% for registered subcontractors, 30% if unregistered) are advance payments towards your eventual Income Tax and NI bill, reconciled when you file your Self Assessment return.
Yes — sole trader CIS subcontractors earning over £50,000 gross must join MTD for Income Tax from April 2026, though CIS deductions themselves are still reconciled at the Final Declaration stage, not quarterly.