Accountancy in Estonia is done usually on a monthly basis, especially if you have a VAT number. That means that you should upload all the purchase and sales invoices for one month before the 5th of the following month.

However, sometimes it might happen that your company buys something and you don’t receive a proper invoice until some time later. What should you do if it becomes a significant amount of time, like one or two months?

Ideally, this should not happen, and you should avoid doing business or purchasing from this type of supplier.

However, if this situation happens occasionally, it is not that problematic. This is the official stance of the Estonian Tax Office:

If the expense document (which meets the requirements of § 37 of the VAT Act) is submitted to the business name for taxable turnover, the VAT paid as input VAT can be deducted from the VAT invoiced for the month in which it is received/posted. The same with receipts without VAT.

So in other words, it is ok if it happens occasionally, but you will have to pay the VAT of the invoice beforehand and won’t be able to recover it until the proper invoice is submitted.