Tropical Montane Forests are unique climate-influenced ecosystems with a vital role for some ecosystem services, of which one of the most important is soil carbon storage. Changes in forest cover affect forest structure, composition and functioning, but little is known about how such changes influence the belowground carbon content. In this study, we addressed this issue by evaluating whether fine-root production differed between forest-cover types and contrasting seasons after controlling arbuscular mycorrhizal fungi (AMF) traits, and what the minimum time required to detect such differences is. We also determined whether AMF-related traits were affected by distinct forest cover and seasons after controlling fine-root production. The objects of study were four forests with distinct degradation histories in the Atlantic Forest: Old-growth, Post-selective logging, Post-clear-cut and Post-pasture forests. Data were collected in four 2500-m2 plots installed in each area and analyzed through multivariate statistics. Fine-root production differed significantly between forest covers, and marginally between seasons, as it was greater in the post-pasture area and in the rainy season. Some AMF traits also differed between forest covers and seasons, especially the abundance of viable spores in the dry season. We found that the shortest period necessary to identify differences in the production of fine roots was over three months. This study shows that forests with different degradation histories and annual climatic variations significantly affect fine-root production and AMF dynamics in Tropical Montane Forests. In particular, ecosystems that have been more perturbed tend to invest more in fine-root production (post-pasture). Our results help to better understand belowground interactions and biomass investment under different managed ecosystems.