Rodents are important hosts for ectoparasites, such as fleas, ticks, and mites, which means they are also important intermediate hosts for many zoonotic diseases. As anthropogenic environments bring humans and rodents into closer contact, an understanding of host–ectoparasite ecology is essential to predict and manage disease spillover risks. We aimed to understand how disturbances in vegetation cover affect rodent ectoparasite diversity, prevalence, spatial segregation, host (i.e., sex, genus, size, and habitat domain), and environmental (i.e., vegetation structure, forest cover, and rainfall) variables in the state of Michoacan, Mexico. We investigated these relationships by trapping rodents in five paired disturbed (reduced vegetation cover and regular human activities) and undisturbed (no reduction in vegetation cover) sites in the summer and autumn of 2022. From 110 trapped rodents, we collected 138 ectoparasites on 38 individuals. We found no difference in rodent diversity, ectoparasite diversity, or ectoparasite prevalence between disturbed and undisturbed sites. However, arboreal and male rodents had a higher probability of carrying ectoparasites than ground‐dwelling and female rodents. Rodents with ectoparasites were not spatially clustered; rather, they were randomly distributed across trapping grids. We also identified two rodent genera (Rattus and Sigmodon) that carry ectoparasites of medical importance and that are in close contact with humans. Our results highlight the necessity of constant monitoring of rodents, ectoparasites, and their associated transmittable diseases. Assessing these interactions and how they are affected by anthropogenic disturbance could better inform management decisions and support the need for rodent conservation programmes in the area.