[2][better source needed] Although the family had ostensibly converted to Christianity, this did not put an end to local antisemitic suspicions.

[3] At the age of eighteen, Isaac was appointed hakham (rabbi) for Beth Israel, one of three Sephardic communities in Amsterdam, which later merged.

In order to be distinguished from his cousin Isaac ben Mattathiah Aboab, he added his mother's last name (da Fonseca) to his own.

In 1642, Aboab da Fonseca was invited by Moses Cohen Henriques appointed rabbi at Kahal Zur Israel Synagogue in Recife, in Pernambuco, Dutch Brazil.

The Portuguese who were animated in part by the Jesuit priest who said "have their open synagogues there, to the scandal of Christianity" calling for the reconquest of the colony and the destruction of the Jews.

Aboab translated from Spanish into Hebrew the works of the kabbalist Abraham Cohen de Herrera, Sha'ar ha-Shamayim and Beit Elohim (Amsterdam, 1655).

[6] In 2007, the Jerusalem Institute (Machon Yerushalaim) in Israel published a book about Rabbi Fonseca's works, including the author's expositions about the community of Recife at that time.