Maria's education was astounding for a woman of her time since her teachers included female scholars, such as humanists Joana Vaz, Luisa Sigeia, and Públia Hortênsia de Castro.

Maria was considered as a second wife for her cousin and half-nephew, the future Philip II of Spain,[10] son of her uncle, Emperor Charles V, and her half-sister Isabella.

The matter was taken under serious consideration from 1549 onward, when her mother settled in Brussels, but these plans were discontinued when Mary Tudor succeeded to the English throne in 1553 and Charles V decided to marry his son Philip to a monarch.

[11][12] Other candidates for her hand were Archduke Maximilian of Austria;[13] his father Ferdinand I, Holy Roman Emperor;[14] James V of Scotland; and the Duke of Savoy.

The original structure she ordered to be built would be completely destroyed in 1681, which would lead to the construction of the new current church, which now serves as the National Pantheon of Portugal.

[16] Eleanor asked her unwed daughter to come and live with her and her aunt Mary, but Maria refused the request and only remained there for three weeks before returning to Lisbon.

During the tumultuous period of the minority of young King Sebastian, a faction of the Portuguese nobility wanted the Duchess of Viseu to replace Queen Dowager Catherine as regent,[citation needed] but these plans came to nothing.