The resurgence of drug-resistant Plasmodium falciparum parasites continues to motivate the development of a safe and efficacious malaria vaccine. Immuno-epidemiologic studies of naturally acquired immunity (NAI) have been a useful strategy to identify new malaria vaccine targets. However, retention of pediatric participants throughout longitudinal studies is essential for gathering comprehensive exposure and outcome data. Within the context of a 3-year cohort (N = 400) study involving monthly finger prick and bi-annual venous blood sample collections, we conducted qualitative surveys to assess factors impacting participant retention. Phase 1 was conducted 3 months after enrollment in July 2018 and phase 2, 12 months later. In phase 1, 236 parents/guardians participated in focus groups and three withdrawn participants and 10 community health volunteers (CHVs) in key informant interviews. Qualitative analysis indicated overall satisfaction with the study, with 61.8% (136/220 respondents) reporting no concerns. Focus group discussants associated attendance with benefits such as improved access to comprehensive healthcare services. Community health volunteers reported concerns over village rumors of inappropriate use of blood samples and dangers associated with venous blood draws. Phase 2 involved 205 parents/guardians and revealed continued satisfaction, with 46.3% (95/205) identifying no concerns, but expressed increasing worries regarding the amount of venous blood sample. This concern was reflected in an uptick of missed visits when venous blood samples were scheduled. Future studies will address parental concerns to determine whether community engagement and education measures increase study retention until completion.