Leisure-time physical activity seems relevant to prevent the development of chronic diseases and obesity. However, not much is known about the economic burden of these healthy behaviors, mainly in longitudinal designs. This study aimed to analyze the impact of walking and cycling on leisure-time on adiposity and healthcare costs among adults. This longitudinal study was conducted at a medium-size Brazilian city and included 198 participants with no missing data attended in the Brazilian Unified National Health System. Cycling and walking were assessed by a questionnaire with a face-to-face interview at four time-points (baseline, 6-month, 12-month, and 18-month). Healthcare costs were assessed using medical records. Adiposity markers included waist circumference and body fatness. Over the follow-up period, participants who were more engaged in cycling presented lower body fatness (p-value = 0.028) and healthcare costs (p-value = 0.038). However, in the multivariate model, the impact of cycling on costs was not significant (p-value = 0.507) due to the impact of number of chronic diseases (p-value = 0.001). Cycling on leisure-time is inversely related to adiposity in adults, whereas its role on preventing chronic diseases seems the main pathway linking it to cost mitigation.