For creating sales invoices for your Estonian company there are several online tools available on the market. None of them are completely free.
For example you can use Envoice, e-Financials or Merit.
Envoice is not an accounting software itself and therefore it has API integrations with e-Financials and Merit. e-Financials or Merit are suitable for micro-company accounting.
Envoice is Estonian made expense management SaaS that has integrations with most popular accounting software in Estonia. It also includes a simple invoicing tool.
Merit is Estonian made accounting software that works perfectly well with Envoice. It makes sense for you to invoice through Merit if your accountant is on the same platform.
e-Financials is Estonian government owned accounting software for micro-companies, one of the cheapest on the market. Not too many accounting firms use it though.
Unicount recommends using Envoice as it is also includes cool expense management tools and is integrated with accounting software that your Estonian accountant would most probably use.