Paleoclimatic variations have profoundly influenced the global distribution of ecosystems and habitats, altering their altitude, spatial configuration, area, and connectivity. Notable examples include island archipelagos and alpine biomes, where shifts in sea-levels and forest lines respectively reshaped their spatial structures. To understand how such changes affected species distributions and biodiversity patterns, we require spatially-explicit reconstructions over continuous time series. However, a comprehensive and reproducible methodology that captures their spatio-temporal dynamism is lacking. Here, we introduce the R package Temporal Altitudinal Biogeographic Shifts (TABS), a tool designed for reconstructing spatial configurations over time, focusing on biogeographic systems bounded by an altitudinal range. We demonstrate the use of TABS by modelling spatial configurations (‘shapes’) of island archipelagos and alpine biomes in response to modulations in sea-levels and forest lines. Unique to TABS, it can also account for crustal deformation due to ice sheet loading and gravitational forces, and for geotectonic and geophysical topographic changes. Beyond past reconstructions, TABS can project spatial configurations shaped by future climatic conditions. This versatile package is easily adaptable to various altitude-bounded biogeographic systems influenced by long-term climatic variations, such as coral reefs and sea shelves. Studying the shifts in biogeographic systems through continuous spatial reconstructions, rather than snapshots in time such as the Last Glacial Maximum, captures the nuances of continuously changing environments and provides a more complete understanding of the biogeography of our planet.