High Andean forests are biodiversity hotspots that also play key roles in the provisioning of vital ecosystem services for neighboring cities. However, they are among the most fragmented and threatened ecosystems in the neotropics. In past centuries, the hinterland of Andean fast-growing cities often experienced a dramatic decline in forested areas, but there are reports that forest cover has been recovering recently. The main aim of this work was to gain a deeper understanding of the forest cover dynamics, together with the effects of anthropogenic perturbations in forest fragments in the Eastern Andean Cordillera of Colombia. Firstly, we analyzed aerial imagery spanning the years 1940 to 2007 from several administrative localities in order to elucidate locality-wide patterns of forest vegetation change. To this aim, we performed image object-based classification by means of texture analysis and image segmentation. We then derived connectivity metrics to investigate whether forest cover trajectories showed an increase or decrease in fragmentation and landscape degradation. Parallely, we characterized the plant communities of high Andean forest remnants in permament forest plots where we gathered data on both the woody vegetation and the understory compositional and structural parameters and compiled a broad array of variables related to anthropogenic disturbance, ranging from local to landscape-wide metrics. Subsequently, in order to filter variables and to test how environmental and anthropogenic variables are affecting the composition, diversity, and aboveground biomass of these forests a series of statistical procedures (NMDS, pRDA and GLMs) were employed. Lastly, we discussed the observed forest cover trend and the local recent history in relation to the compositional and structural parameters examined in the established plots for each locality. Regarding the vegetation cover reconstruction, we observed a forest cover recovery in all the examined localities, except one. In general, forest recovery was accompanied by an increase in core habitat areas. As to the permament plots network, we found that the increase of human-related disturbance resulted in less phylogenetic diversity and in the phylogenetic clustering of the woody vegetation and in lower aboveground biomass (AGB) values. This study provides information on the vegetation composition and structure of peri-urban high Andean forests, while unveiling the long-term dynamics of their cover and connectivity, providing valuable information on historical vegetation changes in a highly dynamic landscape.