VAT quarter does not align to my Year End

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We changed our year end this year from Oct to Dec.  My next VAT quarter is Nov - Jan but I need to run my year end routine in Sage.  Do I reconcile the two months VAT to Dec and then add these onto my 1month period falling in my New FY or will the figures roll over so I can prepare the 3months at the end of Jan?

Just not sure about how the MTD online submission will be affected.

Thanks. 

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