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If you are already on Xero then making the change isn't going to be a huge issue whether you do it now or when you go over the VAT limit. The only difference will be which part of HMRC Xero submits the return to. I don't know how Xero are actually implementing MTD yet as we haven't signed up to their beta but, based on other software, all you'll have to do is tick a box in Xero to tell it to us the MTD APIs rather than the old system.
If it was me I'd go the MTD route from the start just so you don;t have to worry about when you are meant to change over. There are concerns about how robust HMRC's new system is but they are being lenient with late filing fines (note - late filing only, late payment will still be subject to fines) for the first 12 months presumably so no one gets fined for a failure at their end.
The filing screen doesn't let you set dates - it gets those from your HMRC account so I need to do a manual adjustment for my first return I think (some VAT payments I made in the few months prior to registration) so fingers crossed that it all works ok once I hit the button
As long as the pre-registration transaction have been posted with VAT on them in Xero it should pick them up when it calculates the return.
Being cloud-based means I don't have to worry about a hard-disk failure, I can access it on my phone.
I can run a VAT reconciliation report in Xero with manual dates and that picks them up, so it looks like I’ll need to manually add that amount as an adjustment to Box 4 which looks simple enough to do
Edit - mobile site messed up the quoting!
It's possible I've missed something, but I did nose around trying to see how you'd accomplish it and couldn't see a way.
It also appears that if you add an adjustment, then want to amend that adjustment, you can't. eg I entered the wrong manual adjustment, and had to then add a second negative adjustment to correct it - pfft. So yes either Xero is still a bit clunky in this area, or I'm being particularly dumb (both are possible)
Pre-MTD there was a tick box to include late claims but this is gone once you start doing MTD returns. Late claims should now be automatic provided previous returns included late claims.
I'm guessing that it not working for you is a quirk of it being your first return and being an MTD return. You probably will have to put through a manual adjustment to make the claim.
Be careful on your next return though - because it's a manual adjustment the pre-registration expenses won't have been flagged as included on a return so may well end up being included as a late claim on that return so you may need to do the equal and opposite adjustment to avoid claiming anything twice.