On the conclusion of Iberian victory over the Moors, Spain and Portugal extended the conflict against Islam overseas. The Spanish under the Habsburg dynasty soon became the champions of Roman Catholicism in Europe and the Mediterranean against the encroaching threat of the Ottoman Empire. In a similar vein, the conquest of Ceuta marked the beginning of Portuguese expansion into Muslim Africa. Soon, the Portuguese also warred with the Ottoman Caliphate in the Mediterranean, Indian Ocean and Southeast Asia as the Portuguese conquered the Ottomans' allies: the Sultanate of Adal in East Africa, the Sultanate of Delhi in South Asia and the Sultanate of Malacca in Southeast Asia. Meanwhile, the Spanish also went to war against the Sultanate of Brunei in Southeast Asia. The Spanish sent expeditions from New Spain (Mexico) to conquer and Christianize the Philippines, then a territory of the Sultanate of Brunei. Brunei itself was assaulted during the Castilian War. Spain also went to war against the Sultanates of Sulu, Maguindanao, and Lanao in the Spanish–Moro conflict.

Few Muslims were converted to Christianity in the reconquered territories of Iberia, and most were permitted to remain and practise their religion as a protected minority, in effect, reversing the status of Muslims and Christians of the past few centuries. Christians were encouraged to migrate southwards, Arab place names were replaced and many mosques were, naturally, converted to churches, but some remained and Muslim calls to prayer could be heard in many Spanish cities thereafter. The Christian states in Spain became mutually suspicious of each others' intentions with everyone fearing the dominant kingdom of Castile was intent on taking over its rivals. It also proved far from easy for the new states to control their new domains and especially the new class of magnates who prospered there. This may explain why many local military orders were nationalised by the Castilian crown in the second half of the 15th century CE.

Longer-lasting effects of the crusades in Spain included the fostering of an image of Christians as specially favoured to rule, and the idea would persist for many centuries thereafter in the institutions of Spanish government and fuel the religious intolerance that would mark the region in the 15th and 16th century CE. The ideology of the Reconquista and spread of Christianity through violence would also be applied to the Spanish and Portuguese conquests of the New World following Christopher Columbus' voyage of 1492 CE.