[6] The Sephardic Congregation Beth Jaacob ("House of Jacob") in Amsterdam elected him hakham in succession to Moses ben Aroyo.

He was the senior rabbi when the three Amsterdam congregations merged in 1639, outranking Menasseh Ben Israel, and receiving an annual remuneration of 600 guilders.

Morteira was fiercely anti-Christian, while Ben Israel sought to bridge the religious divide between Jews and Christians, particularly dissenting Protestants.

Their feuding prompted the intervention of the Mahamad, the political arm of the community, to prevent the rabbis' disputes from becoming open and a source of instability in the congregation.

[10] Both "held a deprecatory and cynical view of the Law of Moses", doubted the divine nature of Scripture, and argued against the immortality of the soul.

[11] Morteira and Isaac da Fonseca Aboab (Manasseh ben Israel was at that time in England) were members of the Mahamad which on 27 July 1656 pronounced the decree of cherem (excommunication) against Spinoza.

This work (excerpts from which are given in Jacques Basnage, Histoire de la Religion des Juifs) and other writings of Morteira, on immortality, revelation, etc., are still in manuscript.