Is CISflow an AutoEntry alternative?

For the specific job of reading the CIS figures off a subcontractor's invoice, yes — that's exactly what CISflow is built to do. AutoEntry by Sage is broader: it's pay-per-document capture for receipts, supplier invoices and bank statements across any industry. So it isn't really a like-for-like swap. Many practices keep AutoEntry for general capture and use CISflow for the CIS-specific subbie invoices, because the two solve different shapes of the same problem.

Does AutoEntry handle CIS automatically?

AutoEntry extracts the supplier, date, total, line items, nominal and VAT codes very well, and posts a verified draft bill into Xero, Sage or QuickBooks. But it has no CIS-native field: the labour-versus-materials split and the CIS deduction itself aren't read off the invoice. Those are left to the destination accounting software's CIS setup once the bill arrives. CISflow instead extracts the labour/materials split, the rate and the deduction directly from the invoice for you to review.

Why use a CIS-specific tool instead of AutoEntry?

If most of what you process is subcontractor invoices, a CIS-native tool removes the step where you (or your accounting software's CIS setup) still have to separate labour from materials and apply the deduction after the bill lands. If CIS is only an occasional part of a much wider workload, AutoEntry's breadth and per-credit pricing may matter more than CIS depth. It comes down to how much of your month is CIS.

Is CISflow as established as AutoEntry?

No — and we won't pretend otherwise. AutoEntry is a mature product backed by Sage and used widely across UK practices. CISflow is new and in early access. We make up for youth with focus: CIS is the only job we do. You review and approve every extracted figure before anything posts, and we don't file the CIS300 or verify subcontractors with HMRC for you — you stay in control.

Comparison · UK CIS

CISflow vs AutoEntry for CIS invoice extraction

AutoEntry by Sage is a solid, well-liked capture tool. But CIS is a specific job, and AutoEntry doesn't have a CIS-native field — it leaves the split and the deduction to your accounting software. Here's an honest look at where each one fits when the document on your desk is a subcontractor invoice.

The short version

AutoEntry (by Sage) is a mature pay-per-document capture tool. It reads supplier invoices, receipts and bank statements, learns your nominal and VAT codes, and posts a verified draft bill into Xero, Sage or QuickBooks. If your problem is “get every kind of document into the books accurately,” AutoEntry does that job well.

CISflow does one narrow thing: it reads the CIS fieldsoff a subcontractor's invoice — UTR, the labour/materials split, the deduction rate and the deduction amount — so they don't have to be worked out after the bill lands. For the CIS job specifically, that's the difference. For general capture across every supplier, AutoEntry's breadth wins. Many practices will sensibly use both.

Where AutoEntry stops short on CIS

This isn't a claim that AutoEntry is bad — it does general extraction very well. The honest gap is narrower: AutoEntry has no CIS-native field. It captures the invoice as a generic supplier bill, so when the document is a CIS subcontractor invoice:

The labour vs materials split isn't separated out for CIS — it's captured as ordinary line items.
The CIS deduction itself isn't read off the invoice.
Working out the deduction is left to the destination accounting software's CIS setup once the bill arrives.
So someone still has to make sure the supplier is set up as a CIS contact and that the split and rate are applied correctly downstream.

For a contractor or bookkeeper with a stack of different subbie invoices each month, that's real, repeated downstream work — the figures are accurate as general capture, but the CIS-specific part still has to happen somewhere after the bill lands.

Where CISflow is different

CISflow is built around CIS as the job, not a generic one. You forward a subcontractor invoice and it reads the document — PDF, scan or photo — and extracts the CIS fields directly: the UTR, the labour/materials split, the deduction rate, the deduction amount and the net pay. The CIS split is done at the source, not left for the accounting software to figure out afterwards.

Those figures are laid out for you to review and approve — nothing posts silently. On approval, CISflow writes a clean, HMRC-ready CIS bill into Xero (or exports CSV for QuickBooks, Sage and others) and gives you the totals you need for the CIS300. If you want to see exactly what those figures look like, the CIS invoice software guide walks through the whole flow.

Side by side, for the CIS job

This table is scoped deliberately to CIS invoice handling— not the whole product. AutoEntry does far more than CIS; we're only comparing the part that matters when the document is a subbie invoice.

For the CIS job	AutoEntry	CISflow
Reads the CIS deduction off the invoice	No — left to your accounting software's CIS setup	Extracted directly from the invoice
Labour vs materials split for CIS	Captured as generic line items, not a CIS split	Extracted as a CIS split for you to review
CIS-native field	None — generic supplier-invoice capture	CIS is the default behaviour
General capture (receipts, bank statements, any invoice)	Yes — its core strength	No — CIS subbie invoices only
Pricing model	Credit-based, per document	Flat subscription (see pricing)
You review every figure before it posts	Yes	Yes
Files the CIS300 / verifies subcontractors with HMRC	No	No (exports to your accounting software)
Maturity	Established, backed by Sage	New, early access

AutoEntry's behaviour above reflects its published positioning as pay-per-document general capture (current at the time of writing); features change, so check AutoEntry's own docs for the latest. This comparison is limited to CIS invoice handling.

Being honest about CISflow's limits

CISflow is new and in early access, and it deliberately does less than AutoEntry:

It only handles CIS subcontractor invoices — not your general receipts or bank statements.
You review and correct every figure before anything posts. Extraction is good, but it is not a replacement for your eyes, and we won't pretend it is.
It does not file your CIS300 or verify subcontractors with HMRC — you stay responsible for what reaches HMRC.
It's young: fewer integrations and less track record than a tool backed by Sage.

If those trade-offs are deal-breakers, AutoEntry (or your existing setup) may be the right call — and that's a fine answer. CISflow earns its place only when the CIS-specific work after capture is the thing eating your month.

Which one fits you

A simple way to decide:

Mostly subbie invoices, CIS is the pain? CISflow does the CIS split at source instead of leaving it downstream.
CIS is a small part of a much wider capture workload? AutoEntry's breadth probably matters more.
Both? Use AutoEntry for general capture and CISflow for the CIS-specific invoices — they don't conflict.

Want to feel the difference before deciding anything? Use the free CIS deduction calculator — enter labour, materials and the rate, and it returns the deduction, net pay and the CIS300 figures, no sign-up needed.

CISflow is live and in early access. Start free to put a real subbie invoice through it today, and see the extracted CIS fields for yourself.

Keep reading

AutoEntry and Sage are trademarks of their respective owners; CISflow is not affiliated with or endorsed by AutoEntry or Sage. This page is a fair, sourced comparison for the CIS job, not tax advice. CISflow is a data-entry tool, not an accountancy or tax service — you remain responsible for figures submitted to HMRC, and should always verify a subcontractor's status and rate with HMRC.

FAQ

CISflow vs AutoEntry — common questions

Is CISflow an AutoEntry alternative?: For the specific job of reading the CIS figures off a subcontractor's invoice, yes — that's exactly what CISflow is built to do. AutoEntry by Sage is broader: it's pay-per-document capture for receipts, supplier invoices and bank statements across any industry. So it isn't really a like-for-like swap. Many practices keep AutoEntry for general capture and use CISflow for the CIS-specific subbie invoices, because the two solve different shapes of the same problem.
Does AutoEntry handle CIS automatically?: AutoEntry extracts the supplier, date, total, line items, nominal and VAT codes very well, and posts a verified draft bill into Xero, Sage or QuickBooks. But it has no CIS-native field: the labour-versus-materials split and the CIS deduction itself aren't read off the invoice. Those are left to the destination accounting software's CIS setup once the bill arrives. CISflow instead extracts the labour/materials split, the rate and the deduction directly from the invoice for you to review.
Why use a CIS-specific tool instead of AutoEntry?: If most of what you process is subcontractor invoices, a CIS-native tool removes the step where you (or your accounting software's CIS setup) still have to separate labour from materials and apply the deduction after the bill lands. If CIS is only an occasional part of a much wider workload, AutoEntry's breadth and per-credit pricing may matter more than CIS depth. It comes down to how much of your month is CIS.
Is CISflow as established as AutoEntry?: No — and we won't pretend otherwise. AutoEntry is a mature product backed by Sage and used widely across UK practices. CISflow is new and in early access. We make up for youth with focus: CIS is the only job we do. You review and approve every extracted figure before anything posts, and we don't file the CIS300 or verify subcontractors with HMRC for you — you stay in control.