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Background: Chagas disease is one of the most important neglected tropical diseases in the Americas. Vectorborne transmission of Chagas disease has been historically rare in urban settings. However, in marginal communities near the city of Arequipa, Peru, urban transmission cycles have become established. We examined the history of migration and settlement patterns in these communities, and their connections to Chagas disease transmission. Methodology/Principal Findings: This was a qualitative study that employed focus group discussions and in-depth interviews. Five focus groups and 50 in-depth interviews were carried out with 94 community members from three shantytowns and two traditional towns near Arequipa, Peru. Focus groups utilized participatory methodologies to explore the community's mobility patterns and the historical and current presence of triatomine vectors. In-depth interviews based on event history calendars explored participants' migration patterns and experience with Chagas disease and vectors. Focus group data were analyzed using participatory analysis methodologies, and interview data were coded and analyzed using a grounded theory approach. Entomologic data were provided by an ongoing vector control campaign. We found that migrants to shantytowns in Arequipa were unlikely to have brought triatomines to the city upon arrival. Frequent seasonal moves, however, took shantytown residents to valleys surrounding Arequipa where vectors are prevalent. In addition, the pattern of settlement of shantytowns and the practice of raising domestic animals by residents creates a favorable environment for vector proliferation and dispersal. Finally, we uncovered a phenomenon of population loss and replacement by low-income migrants in one traditional town, which created the human settlement pattern of a new shantytown within this traditional community. Conclusions/Significance: The pattern of human migration is therefore an important underlying determinant of Chagas disease risk in and around Arequipa. Frequent seasonal migration by residents of peri-urban shantytowns provides a path of entry of vectors into these communities. Changing demographic dynamics of traditional towns are also leading to favorable conditions for Chagas disease transmission. Control programs must include surveillance for infestation in communities assumed to be free of vectors. Author Summary: Chagas disease affects 8–10 million people in the Americas. Although transmission was previously limited to the rural poor, Chagas increasingly affects urban populations, especially near the city of Arequipa, Peru. We interviewed residents of five communities to learn about why and when they migrated to the city and how their movements may link to Chagas vectors and to explore the settlement patterns of shantytowns and traditional towns. We found that migrants to shantytowns were unlikely to introduce Chagas vectors to the city upon first arrival. Frequent seasonal moves, however, took shantytown residents to valleys surrounding Arequipa where vectors are prevalent. In addition, the settlement pattern of shantytowns and the practice of raising domestic animals create a favorable environment for vectors. Finally, population loss and replacement by low-income migrants in one traditional town has created the human settlement pattern of a shantytown. This study exposes potential links between population dynamics and Chagas vector infestation. Suggested methods for improving vector control include focusing future vector surveillance in areas with mobile populations, creating educational campaigns for migrant workers to Chagas-endemic areas, and fomenting collaboration between the Arequipa Ministries of Health and Housing to ensure the inclusion of new shantytowns in vector surveillance. [ABSTRACT FROM AUTHOR]