Following her expulsion, she lived the remainder of her life as Sor Magdalena, a nurse for Daughters of Charity Services in New Orleans, eventually rising to the position of Mother Superior for that congregation.
Favez remained in Paris and took up the study of medicine at the Sorbonne, taking on the dress and identity of a male army officer with her deceased husband's rank.
After Favez's graduation, she worked as a French army surgeon during the Napoleonic Wars, allegedly alongside her uncle, until she was captured by Wellington's forces in Spain, and imprisoned.
Forcible examinations by local doctors revealed her sexual anatomy, and several accusatory letters allegedly written by Juana de Léon surfaced throughout her trial.
Following her second recorded suicide attempt, Favez was barred from the institution, as well as the Spanish territories, and placed on a ship to New Orleans, where she joined the Daughters of Charity Services as a nun.
Favez's story is documented in several books, including For Dressing Like a Man by Cuban historian Julio Cesar Gonzáles Pagés, whose publication was supported by the Swiss Agency for Development and Cooperation.