Da Costa also occupied an ecclesiastical office. While a student of canon law, he began to read the Bible and contemplate it seriously. He was aware that his family had Jewish origins, and in the course of his studies, he began to consider a return to Judaism. After his father died, he began to very carefully reveal his newfound sentiments to his family. Ultimately, in 1617, the whole family decided to return to Judaism; they fled Portugal for Amsterdam, which would soon become a thriving center of the Sephardic diaspora.
However, upon arriving in the Netherlands, Da Costa very quickly became disenchanted with the kind of Judaism he saw in practice there. He came to believe that the rabbinic leadership was too consumed by ritualism and legalistic posturing. In 1624 he published a book titled An Examination of the Traditions of the Pharisees which questioned the fundamental idea of the immortality of the soul. Da Costa believed that this was not an idea deeply rooted in biblical Judaism, but rather had been formulated primarily by the Rabbis. The work further pointed out the discrepancies between biblical Judaism and Rabbinic Judaism; he declared the latter to be an accumulation of mechanical ceremonies and practices. In his view, it was thoroughly devoid of spiritual and philosophical concepts.
The book became very controversial and was burned publicly. Da Costa was called before the rabbinic leadership of Amsterdam for uttering blasphemous views against Judaism and Christianity. He was fined a significant sum and excommunicated.
He ultimately fled Amsterdam for Hamburg, Germany (also a prominent Sephardic center), where he was ostracized from the local Jewish community. He did not understand German, which further compounded his difficulties. Left with no place to turn, in 1633 he returned to Amsterdam and sought a reconciliation with the community. He claimed that he would go back to being "an ape amongst the apes"; he would follow the traditions and practices, but with little real conviction.
However, he soon again began to express rationalistic and skeptical views; he expressed doubts whether biblical law was divinely sanctioned or whether it was simply written down by Moses. He came to the conclusion that all religion was a human invention. Ultimately he came to reject formalized, ritualized religion. In his view, religion was to be based only on natural law; God had no use for empty ceremony. In many ways his beliefs were Deistic; he believed that God resides in nature, which is full of peace and harmony, whereas organized religion is marked by blood, violence, and strife.
Eventually da Costa came across two Christians who expressed to him their desire to convert to Judaism. In accordance with his views, he dissuaded them from doing so. For the communal leadership of Amsterdam, this was the final straw. He was thus again excommunicated. For seven years he lived in virtual isolation, shunned by his family and loved ones. Ultimately, the loneliness was too much for him to handle, and he again returned to Holland and recanted.
As a punishment for his heretical views he was publicly given thirty-nine lashes at the Portuguese synagogue in Amsterdam. He was then forced to lie on the floor while the congregation trampled over him. This left him so demoralized and depressed that he was unable to live with himself. After writing his autobiography, Exemplar Humanae Vitae (1640), in which he wrote about his experience as a victim of intolerance, he set out to end the lives of both his cousin and himself. Seeing his relative approach one day, he grabbed a pistol and pulled the trigger. It misfired. Then he reached for another, turned it on himself, and fired, dying, they said, a terrible death.
Ultimately there are many ways to view Uriel da Costa. He has been seen as a crusader of free thought and an early precursor of modern biblical criticism. Internally to Judaism, he was seen by many as both a troublemaking heretic and martyr against the intolerance of the Orthodox Jewish establishment. He has also been seen as a precursor to Baruch Spinoza.
Da Costa is also indicative of the difficulty that many Marranos faced upon their arrival in an organized Jewish community. As a Crypto-Jew in Iberia, he read the Bible and was impressed by it. Yet upon confronting an organized Rabbinic community, he was not equally impressed by the established ritual and religious doctrine of Rabbinical Judaism, such as the Oral Law. As da Costa himself pointed out, traditional Pharisee and Rabbinic doctrine had been contested in the past by the Sadducees and the Karaites.