Rhipicephalus microplus infestations are a major concern for cattle production in neotropical regions. Anti-tick vaccines represent a sustainable alternative to chemical acaricides; however, improving vaccine efficacy remains challenging. This study evaluated the protective efficacy of polypeptide-based formulations of pBm86 and pSubolesin administered as co-immunization or as a cocktail in naturally infested cattle. Twelve calves were assigned to three groups: G1: 100 μg pBm86 + 50 μg pSubolesin co-immunized; G2: same formulation in cocktail; and G3: control. The cocktail significantly reduced adult female tick numbers, oviposition, and larvae hatching (p < 0.05), achieving a vaccine efficacy of 75%. In contrast, co-immunization achieved 50% efficacy. Vaccinated cattle developed significantly increased antigen-specific IgG levels against Subolesin than Bm86. IgG antibodies recognized native tick proteins by Western blot, and their efficacy was confirmed in vitro using blood-feeding assays. These results indicate that the cocktail formulation showed improved efficacy compared with co-immunization in this study, possibly by affecting complementary biological processes in ticks. Finally, this study supports the development of multi-antigen, polypeptide-based vaccines as a promising and sustainable approach for the control of R. microplus under natural field conditions.