Fernandes was born in São Paulo Paulo and raised in Santana do Parnaíba. He married Maria de Zunega of Paraguay, daughter of Bartolomeu de Torales with whom he had a daughter, Mary Torales. After being widowed, married Isabel de Proenca, daughter of João de Abreu who had twelve sons.
He began as a bandeirante (or pioneer) who would gather natives in Rio Grande do Sul and Paraguay to work in the fields. Around 1654, Fernandes built a house on the edge of the Sorocaba River and a chapel—Nossa Senhora da Ponte—known today as Sorocaba Metropolitan Cathedral. On 21 April 1660 he donated land, plantations and indigenous slaves to the Benedictines.
This later became the foundation of the Monastery of Saint Benedict (Mosteiro de São Bento).
In 1661, Baltazar Fernandes went to São Paulo to talk to the governor general Salvador Corrêa de Sá e Benevides. Fernandes wanted Sorocaba to cease being a village and turned into a vila (the name given to cities at the time).
The governor granted his request and, on 3 March 1661, Sorocaba was elevated to the category of Vila (or town). The full name became the Vila de Nossa Senhora da Ponte de Sorocaba.
According to the historian Anita Novinsky, Fernandes, as well as many other pioneers, was Jewish and a "New Christian" (cristão-novo).
According to one account, Fernandes shot Father Diogo de Alfaro in the head after the Portuguese Inquisition sent him to investigate the Paulista "heretics".
Sorocaba immediately started a city council and that same day, they named the main members of the board: Judges Baltazar Fernandes and André de Zunega, Aldermans Cláudio Furquim and Paschoal Leite Paes, and Attorney Domingos Garcia, accompanied by Registrar Francisco Sanches.
