After this tutor was appointed a bishop in June 1533 he arranged that Commandino be appointed as private secretary to Pope Clement VII. He took up this appointment in June 1534 but on 25 September 1534 Pope Clement died and Commandino then went to the University of Padua. Bernardino Baldi, who was a student of Commandino in the latter part of his life and wrote a short biography of him in 1587, claimed that he studied philosophy and medicine at Padua from 1534 to 1544 but one should not suppose that this means that he was a student for ten years.
Pagkatapos na ito tagapagturo ay hihirangin ng isang obispo sa Hunyo 1533 siya inayos na Commandino ay hinirang bilang pribadong secretary sa Papa mainam VII. He took up na ito appointment sa Hunyo 1534 ngunit sa 25 Setyembre 1534 Papa mainam namatay at Commandino pagkatapos ay nagpunta sa Unibersidad ng Lungsod ng Padova. Bernardino Baldi, na noon ay isang mag-aaral ng Commandino sa huling bahagi ng kanyang buhay at wrote isang maikling talambuhay ng 1587 sa kanya, inaangkin na siya-aral ng pilosopiya at gamot at Padua 1534-1544 ngunit ang isa ay hindi dapat ipagpalagay na ito ay nangangahulugan na siya ay isang mag-aaral para sa sampung taon.