Aagesen was appointed organist of Vor Frue Kirke in Copenhagen on 23 June 1593.
[3] In 1600, he went to Prague as a royal commissioner for the King Christian IV.
Between 1609 and 1611, he is supposed to have taught at the court and therefore received subsidies from the royal treasury.
In 1613, the Danish king published a letter stating that all men of the "Roman Catholic" religion must leave Denmark.
Aagesen, who had been suspected of being on the Pope's payroll as early as 1604, was informed of a ruling made in the governing body of Copenhagen University on 15 September 1613 that, since he had Catholic sympathies, he should not be allowed to continue as organist.