Evaluating the cumulative effects of the human footprint on landscape connectivity is crucial for implementing policies for the appropriate management and conservation of landscapes. We present an adjusted multidimensional spatial human footprint index (SHFI) to analyze the effects of landscape transformation on the remnant habitat connectivity for 40 terrestrial mammal species representative of the Trans-Mexican Volcanic System in Michoacán (TMVSMich), in western central Mexico. We adjusted the SHFI by adding fragmentation and habitat loss to its original three components: land use intensity, time of human landscape intervention, and biophysical vulnerability. The adjusted SHFI was applied to four scenarios: one grouping all species and three grouping several species by habitat spatial requirements. Using the SHFI as a dispersal resistance surface and applying a circuit theory based approach, we analyzed the effects of cumulative human impact on habitat connectivity in the different scenarios. For evaluating the relationship between habitat loss and connectivity, we applied graph theory-based equivalent connected area (ECA) index. Results show over 60% of the TMVSMich has high SHFI values, considerably lowering current flow for all species. Nevertheless, the effect on connectivity of human impact is higher for species with limited dispersal capacity (100–500 m). Our approach provides a new form of evaluating human impact on habitat connectivity that can be applied to different scales and landscapes. Furthermore, the approach is useful for guiding discussions and implementing future biodiversity conservation initiatives that promote landscape connectivity as an adaptive strategy for climate change.