For many of the exiles, the best immediate option was to cross the border overland to Portugal. The Jews who did so were accepted by the Portuguese king João II for pragmatic reasons. For a sum of 100 cruzados, he offered a wealthy family the right to reside permanently in Portugal. He also welcomed skilled craftsmen. He required most of the refugees, however, to pay eight cruzados per person for the right to remain in Portugal for eight months, after which time they would have to embark for other lands. When the time came for their departure, the king limited the ships available, and only some of the refugees were able to leave, moving on to Mediterranean destinations where other exiles had settled.
If the remaining Jews believed they had found a haven in Portugal, they were soon disabused. João’s successor Manuel I (1495-1521) found himself in a dilemma. Ferdinand and Isabella of Spain had offered him their daughter’s hand in marriage – a great political opportunity – but they placed a condition on the union- the expulsion of the Jews from Portugal. The young Portuguese monarch, not wanting to give up the match, ordered the expulsion of the Jews from his kingdom by November 1497. He expected and hoped that mass conversions would ensue, allowing the economically beneficial Jewish population to remain. But the population of Jews who had already sacrificed so much to resist baptism showed no eagerness to comply. In early 1497 the king thus rounded up Jewish children and had them forcibly baptized, a measure aimed at preventing their parents from fleeing. The order then went out for the Jews to gather in Lisbon prior to their departure. Jews flooded into the city with the expectation that they would be put on board ships. But instead they, too, were forcibly baptized. To prevent these new conversos from leaving his kingdom, the king, in the spring of 1499, prohibited their emigration.
It was obvious to everyone that the conversos of 1497 would not become sincere Catholics at once. However, it was Manuel’s expectation that in the course of time the converso population would be integrated into Portuguese society. This is evident from his decree of 1497- “For the next 20 years no Inquisition shall act against them [the conversos]. They may live freely and without fear, and in the course of this period they will abandon their habits and will be strengthened in our holy faith.” But in fact the New Christian population of Portugal proved to be particularly tenacious in its Jewish loyalties. Because of its particular cohesiveness and its relatively high proportion of judaizers, it was to become a somewhat distinct entity in the Sephardic diaspora.

Rioting against the Portuguese New Christians first broke out in Lisbon in May, 1504. Two years later, in 1506, during an outbreak of plague exascerbated by drought, and shortly after some New Christians had been accused of celebrating Passover, violence again broke out in Lisbon. This time more than a thousand New Christians were killed – a massacre that left the New Christians terrified. The king issued an edict in 1507 that finally allowed New Christians to leave Portugal freely. Many did. Yet most stayed.

In 1531 Manuel’s successor, João III, began negotiations with the pope to obtain permission to establish an Inquisition like that of Spain in Portugal. The conversos reacted sharply, and acted by means of “lobbyists” in Rome to thwart the program. As a result of their efforts, as well as hesitations on the part of the Vatican, an Inquisition was established in Portugal only in 1536. But once it became active (the first auto-da-fé was held in Lisbon in 1540), the Portuguese Inquisition proved acted vigorously to punish “judaizers.” The prohibition for conversos to leave the kingdom had been renewed in 1521, but royal decrees never entirely impeded emigration. Indeed, the emigration of Portuguese conversos – and their reversion to Judaism in Jewish communities outside the Peninsula – played an important role in the development of the Sephardic diaspora, as we shall see.