After Bartholin's death in 1690, Árni became librarian and secretary to a Danish statesman, Matthias Moth, brother of the king's mistress, Sophie Amalie Moth. From late 1694 to late 1696, he was in Germany, primarily to assess a book collection that had been offered to the university, but he extended the stay. Meanwhile, presumably thanks to his employer, he was appointed a professor designate at the university, and since he had never published, while still in Leipzig he published an edition of some Danish chronicles that he had copied while working for Bartholin. When he returned to Denmark, he resumed working for Moth but in 1697 was also appointed secretary at The Royal Secret Archives (Det Kongelige Gehejmearkiv). In 1699 he published anonymously, at Moth's request, an account of a witchcraft case in which Moth had been a judge, "Kort og sandfærdig Beretning om den vidtudraabte Besættelse udi Thisted".