Payroll in Jan will be nil because is run quarterly and next one is due in March. There is a refund due from HMRC of £5k re CIS suffered for which an EPS was sent last month. There will be a submission for CIS subcontractors in Jan - and therefore PAYE will be due even if not actually paid over.
Should I run an EPS at the end of Jan to show nothing on the payroll? I suspect I should but can't decide.
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If the payroll is run quarterly, it cannot be an Annual Scheme, so I trust that you have filed a nil FPS/EPS for each of the 6 months to date in 2016/17 in which no salary has been paid. Why would you then not file a nil FPS/EPS for January and February when there will also be no salary payments?
When you have employees who have been notified to HMRC as being on the payroll, which you must have if the same employee(s) are paid each quarter, you would normally file a nil FPS, rather than an EPS to say that no-one has been paid.