He was accused by the Portuguese Inquisition of Judaism and his trovas were included in the catalogue of forbidden books, since they aroused interest especially among the new Christians.

He faced this tribunal, which deemed him innocent, but he was forced to participate in the 1541 auto-da-fé procession and also to stop interpreting the Bible or writing on theology.

It was edited by D. João de Castro (sebastianist grandson of the famous namesake Vice-Roy of Portuguese India).

The "Trovas do Bandarra" influenced the sebastianist and messianic thought of Priest António Vieira and Fernando Pessoa.

Bandarra's prophetics includes three points: the Fifth Empire, the going and return of the Encoberto [Covered One] (after Alcácer-Quibir identified as being el-rei D. Sebastião) and the destinies of Portugal.