With the guidance of local Piarists, Șaguna's parents had opted to convert to Roman Catholicism, seeking to obtain a better status than the second-class one reserved for most Eastern Orthodox subjects of the Habsburgs.

The respect he enjoyed, as well as his will for mediation got him elected to the executive of the Romanian movement, and soon after he was to be the main delegate petitioning Emperor Ferdinand I of Austria and the Vienna government.

Austrian General Anton Freiherr von Puchner, who had taken refuge to the Wallachian region of Oltenia, pressured Șaguna and other leaders to openly demand that Imperial Russian occupiers of Wallachia protect his last contingents as they evacuated Transylvania.

In February 1849, as the tide of a second and decisive Russian military action grew near, Andrei Şaguna left for Austria, where he drew suspicion by trying to reanimate a previous project, which asked for a common Romanians-in-Austria realm (Transylvania together with the Banat and Bukovina).

Such demands proved decisive after the crushing of Kossuth's movement: Austria steadily withdrew its offers to Romanians, as it feared that encouragement of their cause would lead to a Hungarian-like crisis.

In 1850, Șaguna was again leader of a delegation to Vienna, asking Franz Joseph I of Austria for an institution of higher learning to be approved by the Austrian leadership, and further liberties and education rights for the Romanian community.