When he arrived back in Jerusalem Hezekia opened the doors of Yeshivat Bet Yaakov. Da Silva had secured the ongoing support of the Dutch philanthropist Israel Jacob Pereira while in Amsterdam, and in Pereira's honor the yeshiva was renamed Bet Jacob Pereira. Da Silva took a decided interest in the controversy that took place between Moses Hagiz and Judah Vega. However, his death in Jerusalem in 1695 at age 39 cut short his activity in behalf of the former. He was buried at the foot of Mount of Olives.