Land-use change is a primary driver of biodiversity loss. Tropical ecosystems face rapid conversion rates due to the encroachment of agricultural lands and supply needs for goods and services from an increasing population and changing market demands. Measuring the effect of land conversion on species diversity is challenging due to incomplete and uneven knowledge of different taxonomical groups. Here, we contrast different metrics for measuring biodiversity loss across three land-use typologies: secondary forest, agroforestry, and monoculture for five taxonomic groups: birds, frogs, fish, dung beetles, and macroinvertebrates in the Andean piedmont forests of the western equatorial Andes. Albeit our limited and uneven sample in space and time, we found that rarity, Non-Metric Multidimensional Scaling, and Multinomial Classification Model (i.e., classifications of habitat specialists and generalists) constitute a more sensitive set of indicators to assess land-use change impacts on tropical mountain biodiversity compared to classical metrics. Likewise, our results showed that land-use intensification influenced community assemblages in the five taxonomic groups. These non-classical biodiversity metrics can provide better insight into the effect of land conversion on these highly biodiverse ecosystems composed of many rare species.