Recorded performances, in which Cenčić was either treble soloist of the Sängerknaben or an independent male soprano, include Handel's Messiah, Haydn's Die Schöpfung, and Mozart's Requiem, alongside countertenor Derek Lee Ragin).

He is noted for a series of dramatically varied portrayals, including the female role of Saint Alexis' wife (Sposa) in Stefano Landi's 1631 opera Il Sant'Alessio, with William Christie and Les Arts Florissants.

Cenčić also appeared in the role of Perseo in the serenata Andromeda Liberata, attributed to Antonio Vivaldi but of dubious authorship, both in a world tour and a recording on the DGG Archiv label with Andrea Marcon and the Venice Baroque Orchestra.

[3] A studio recording of operatic arias by George Frideric Handel, notably containing music composed for the mezzo-soprano castrato Giovanni Carestini, was released on the EMI/Virgin label in the UK on 1 March 2010.

In 2017, he performed the same role in the production for the reopening of the Staatsoper Unter den Linden in Berlin, staged by Eva Höckmayr, conducted by Diego Fasolis, alongside Anna Prohaska as Poppea.