Vector control is usually designed as a top-down system with minimum capacity to respond to specificities of epidemiological settings at fine scale or to adjust to routine stressors. Here, we investigated barriers in Chagas disease vector surveillance and control systems in Arequipa, Peru. We conducted in-depth interviews and focus groups with key stakeholders (n=32) at different levels of the health system and community, using process maps to illustrate the workflow for passive and active surveillance. We identified barriers at each step of the process, including systemic, operational, financial, and policy limitations. For passive surveillance, barriers in community participation to report infestations were linked to challenges in capturing the vector and bringing it to a health facility or community health worker. Amongst systemic barriers were related to the use of a data system that did not meet the needs for recording and managing data on vector control activities. At the policy level, the establishment of quotas on the number of houses staff needed to inspect ignores important determinants for infestation and lacks an appropriate sampling design. We discuss the impact of the reported barriers to effective conduction of surveillance and control activities and the initiatives and strategies that have been designed and assessed to bridge these gaps in order to collaboratively design a more resilient health system.