One of the notable achievements of John III's reign was the Portuguese colonization of Brazil. The king focused on strengthening Portugal's bases in India, such as Goa, which secured Portugal's monopoly over the spice trade from the Maluku Islands. Portuguese explorers also made significant discoveries during this time, including the first European contact with Japan.

John III pursued a policy of abandoning Muslim territories in North Africa in favor of trade with India and investments in Brazil. This decision was driven by economic considerations and the increasing threat posed by the Ottoman Empire. By redirecting resources to these more lucrative regions, John III aimed to bolster Portuguese trade and secure Portugal's position as a major player in the global economy.

In terms of international relations, John III forged alliances with major European powers through strategic marriages. His sister Isabella of Portugal married Charles V, the king of Spain and Holy Roman Emperor, strengthening Portugal's ties with the Spanish Habsburgs. John III himself married Catherine of Austria, Charles V's younger sister. These alliances ensured peace in the Iberian Peninsula for a number of years.

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John III also maintained close relations with the Papal States and played a significant role in the Counter-Reformation. He introduced the Inquisition in Portugal and strengthened the Catholic Church's influence in the country. The king appointed family members and trusted individuals to important religious positions, including his brothers Henry and Afonso as Cardinals.

Under John III's patronage, Portugal experienced a flourishing of arts and culture. The king supported renowned figures such as Gil Vicente, Garcia de Resende, Sá de Miranda, and Luís de Camões. He also promoted scientific endeavors and education, establishing scholarships for Portuguese students abroad and relocating the Portuguese university from Lisbon to Coimbra.

John III's rule was not without challenges. The Portuguese Empire, with its vast territories and extensive trade networks, was difficult to administer and burdened with debt. The administration of overseas territories faced issues of corruption and mismanagement, which led to a decline in Portugal's trade monopoly. The empire also faced threats from the Ottoman Empire and rival European powers.

Despite these challenges, John III's reign left a lasting impact on Portugal's colonial expansion, cultural development, and diplomatic relations. His policies and decisions shaped the course of Portuguese history and contributed to the country's status as a global power during the Age of Discovery.