Stamp duty is charged on the acts, contracts, documents and other events listed in the General Stamp Duty Table (Tabela Geral do Imposto do Selo). Acquiring ownership of real estate for consideration falls under item 1.1 of that table and is charged on the value, in addition to IMT. The rate applied is 0,8 %.
In practice
On a purchase, stamp duty is assessed at the same time as IMT and on the same base: whichever is higher of the contract value and the taxable value. It is small next to IMT, but it belongs in the cash a buyer needs ready before the deed.
A first purchase of an own permanent home by a buyer aged up to 35 carries a deduction against this item, set out in the Stamp Duty Code, capped by the top of the first band of the table for those buyers. The flatin.pt IMT calculator shows the duty charged and, where it applies, the deduction on a separate line, so the total can be checked by eye.