The relocation of indigenous populations to inter-Andean valleys under Toledo's policies led to the foundation of several Andean cities, which contributed to urban development in colonial Peru . However, this also introduced long-term socio-economic disruptions as traditional agricultural practices and social structures were dismantled, resulting in diminished agricultural productivity and heightened susceptibility to natural disasters like landslides . These changes imposed by the Spanish administration laid the groundwork for the socio-political configuration of colonial and modern Andean cities, influencing urbanization patterns long after the colonial period .

Viceroy Francisco de Toledo implemented social reforms, such as the Reducciones, primarily to exert better control over the indigenous population. By relocating indigenous people from the high mountains to valleys, the Spanish authorities could more easily enumerate the population for taxation, labor (mita), and religious conversion . The social consequences included a significant disruption to the traditional social structure of the indigenous people. While new Andean cities were founded, the relocation put the population at risk of natural disasters, such as mudslides, and led to the abandonment of ancient agricultural terraces, diminishing the agricultural frontier .

Viceroy Toledo consolidated Spanish authority through bureaucratic and legal reforms by emphasizing strict hierarchical control and ensuring that laws from the Spanish Crown were enforced over those of local governance bodies such as the Audiencias . He implemented measures to ensure respect for Spanish officials among the colonists and regulated the behavior of colonial administrators to prevent corruption . These reforms minimized internal dissent and strengthened the Crown's authority, making it difficult for uprisings or rebellions to gain traction, as any deviation from the directive was met with harsh consequences, exemplified by the military action against Túpac Amaru I .

Viceroy Toledo's collaboration with writers like Pedro Sarmiento de Gamboa played a crucial role in crafting cultural narratives that sought to validate Spanish colonial rule by portraying the Incas negatively. By financing Sarmiento de Gamboa's 'Historia Indica,' Toledo aimed to depict the Inca Empire as oppressive to justify the conquest and promote the idea that Spanish rule was a civilizing force . This narrative strategy was designed to shift perceptions away from seeing the Incas as benevolent rulers, thereby framing the Spanish regime as a necessary and rightful authority. This reimagining of history served both to reinforce Spanish legitimacy and counteract earlier accounts that could undermine colonial authority .

The political intent behind negotiating with Túpac Amaru I was to legitimize Spanish rule by integrating the last Inca into the colonial structure through settlements and titles . However, Túpac Amaru's execution of Toledo's representative forced Toledo to assert authority through military means . By executing Túpac Amaru I, Toledo aimed to demonstrate the uncompromising strength of his rule, crucial for maintaining order and preventing future insurrections during the early and unstable period of his governance .

Viceroy Toledo's reforms are controversial because they imposed order while also being oppressive. On the one hand, his reforms solidified colonial institutions and established control over the indigenous population, bringing order and efficiency to resource extraction, such as in the case of the mita system and economic regulation of mines . On the other hand, these same reforms disrupted traditional indigenous life, resulted in harsh labor conditions, and reflected the authoritarian and exploitative nature of colonial rule . Consequently, Toledo is praised for bringing stability and criticized for the severe societal impact on indigenous populations and enforcement of the colonial regime's harsh policies.

Viceroy Toledo's governance reflected colonial authoritative structures by centralizing power in the viceroy's office, enforcing strict oversight over Spanish officials, and ensuring the application of laws from the Spanish Crown above all local councils or Audiencias . His reforms, such as relocating indigenous populations for easier control and organizing labor for mita, reinforced Spanish economic interests . Toledo's strict enforcement of colonial order, including through military action against rebel leaders like Túpac Amaru I, consolidated Spanish control over Peru and ensured the Crown's economic and political objectives were met .

Sarmiento de Gamboa's works, commissioned by Viceroy Toledo, aimed to reshape the perception of the Inca Empire by emphasizing its negative aspects. This effort was motivated by a need to justify Spanish colonial rule and downplay previous portrayals that depicted the Incas in a positive light . By presenting the Incas as tyrannical and oppressive, Toledo's government sought to depict Spanish conquest as a liberating force, thus altering the historical narrative to support colonial legitimacy and diminish the nostalgia for pre-Spanish governance among indigenous and academic audiences .

Viceroy Toledo's economic policies, particularly regarding the Huancavelica mercury mines, were designed to maximize economic benefit for the Spanish Crown. He declared these mines to be worked for the exclusive benefit of the Crown, reflecting the mercantilist priorities of maximizing resource extraction and enrichment of the mother country . This approach was typical of colonial priorities, focusing on transferring wealth from the colonies to Spain, often at the expense of local social welfare.

The establishment of the Santa Inquisition under Viceroy Toledo had a significant impact on the social fabric of Spanish and mestizo communities in Peru. By targeting Spanish whites and mestizos, the Inquisition sought to enforce Catholic orthodoxy and eliminate liberal behaviors considered contrary to Church teachings . Although it did not apply to indigenous peoples, its establishment created an environment of fear and enforced conformity among those educated in Christian doctrines . This contributed to a more rigid and controlled colonial society.