At some point in time, his family moved to Amsterdam where he studied at the De los Pintos rabbinical academy in Rotterdam.
On 3 May 1655 Abendana delivered a famous memorial sermon on the Cordovan martyrs Marranos Nunez and Almeyda Bernal who had been burned at the stake.
Several years later, with his brother, Isaac, Jacob published the Bible commentary Miklal Yofi by Solomon ben Melekh which included his own commentary, Lekket Shikchah (Gleanings), on the Pentateuch, the Book of Joshua, and part of the Book of Judges.
Over the following years, he completed a Spanish-language translation of the Mishnah, along with the commentaries of Maimonides and Obadiah of Bertinoro.
Jacob Abendana died in London in 1685 and was buried in the Portuguese cemetery at Mile End.