To process a CIS payroll, the CIS module needs to be enabled. If you don't have access to the CIS module, please contact us for information on how to activate it.

Page Contents

Your Workflow Guide

The process outline displayed on this page will take you through the minimum steps required to complete a standard CIS payroll.

	Category	App	Menu	Description	Help
1	Review	InTime	Timesheets > Approved	Check timesheets are in and approved
2	Export	InTime	Timesheets > Export	Select payroll frequency and export (This will include timesheets and expenses)	?
3	Export	InTime	Notification bell	Wait for confirmation that all timesheets exported sucessfully
4	HMRC: CIS Verification	InPay Manual	Processes > HMRC Submission or CIS > Worker: Verification No	Generate and send a new CIS Verification type Manually verify (through HMRC gateway or employer helpline) - Add verification number to worker record	?
5	Payroll Update: Ad hoc	InPay	CIS > Adjustments	Add any ad hoc (one off adjustments) - Example: Advance deduction	?
6	Review	InPay	Reports > Standard Reports: Category: Employee\| Report: Employee Notes Category: Employee \| Report: Exceptions New Category: Pay \| Report: Pay Summary Detailed Category: Employee \| Report: CIS Worker List	Here is a selection of the most common reports used to review payrolls: A report summarising all employee notes entered Reports on exceptions configure through COMPANY > GENERAL A gross to net report containing totals of payments and deductions made Contains a list of CIS workers, their current deduction status, UTR and verification number	?
7	Payroll: HMRC	InPay	Processes > HMRC Submission:	Submit your CIS monthly return (once per month)	?
8	Payroll Update: Close	InPay	Payroll > Payroll Processing	Commit your payroll in to the next period	?
9	CIS Deduction Sync	InTime	Settings: InPay Settings > Synchronise payslips	Update InTime timesheets with CIS deduction values
10	InTime: Self-Bill generation	InTime	Pay > Generate Invoices	Generate your CIS invoices (You can isolate CIS timesheets by using the payroll filter under the “Advanced” tab)
11	InTime: Self-Bill delivery	InTime	Pay > List invoices (sent status: No)	Click all undelivered purchase invoices (You can isolate CIS invoices by using the payroll filter under the “Advanced” tab”)
12	InTime: BACs	InTime	Pay > Generate Payments	Consolidate your purchase invoices in to a single payment batch (download the payment format and upload to your bank) [Optional] Deliver remittance advices created by the payment batch	?

Frequently asked questions

In addition to the above, we have also provided some answers to the most frequent questions asked.

My contractor’s past payments were deducted at 30% (or higher rate), they are now CIS registered with a 20% deduction rate. Can I back date the Tax treatment to the correct amount?

No. Assuming you have re-verified the contractor, you should adjust the contractor record to the 20% CIS tax status on InPay. Any future payments will be deducted at the new rate.

You and the contractor should consult with HMRC directly regarding any deduction overpayments made.

I need to re-verify a contractor through InPay, how do I do this?

Contractors can be re-verified through InPay by removing any stored verification number from their record. Records without any verification numbers will automatically be included in your next CIS verification request.

Caution should be applied when removing any verification numbers. For example, this approach should only really be used when a verified contractor has not been paid for more than 2 years.