Habitat loss and soil organic carbon (SOC) stock variations linked to land-cover change were estimated over two decades in the most densely populated biodiversity hotspot in the world, in order to assess the possible influence of conservation practices on the protection of SOC. For a study area of 88 484 km2, 70% of which lie inside the Western Ghats Biodiversity Hotspot (WGBH), land-cover maps for two dates (1977, 1999) were built from various data sources including remote sensing images and ecological forest maps. SOC stocks were calculated from climatic parameters, altitude, physiography, rock type, soil type and land-cover, with a modelling approach used in predictive learning and based on Multiple Additive Regression Tree. The model was trained on 361 soil profiles data, and applied to estimate SOC stocks from predictor variables using a Geographical Information System (GIS). Comparison of 1977 and 1999 land-cover maps showed 628 km2 of dense forests habitat loss (6%), corresponding to an annual deforestation rate of 0.44%. This was found consistent with other studies carried out in other parts of the WGBH, but not with FAO figures showing an increase in forest area. This could be explained by the different forest definitions used, based on ecological classification in the former, and on percentage tree cover in the latter. Unexpectedly, our results showed that despite ongoing deforestation, overall SOC stock was maintained (∼0.43 Pg). But a closer examination of spatial differences showed that soil carbon losses in deforested areas were compensated by sequestration elsewhere, mainly in recent plantations and newly irrigated croplands. This suggests that more carbon sequestration in soils could be achieved in the future through appropriate wasteland management. It is also expected that increasing concerns about biodiversity loss will favour more conservation and reinforce the already prevailing protective measures, thus further maintaining C stocks.