Clay minerals formed during soil formation are imprints of ecosystem functioning and pedogenic processes in landscapes. The study evaluated the variations in taxonomy, soil weathering and pedogenic changes in contrasting forest soils in the Southern Western Ghats, India. Three different forest systems with comparable soil-forming factors vis-a-vis evergreen, moist deciduous and a man-made system (rubber plantation) were evaluated for physical, chemical, morphological, and pedogenic characteristics of the related soils. Soil profiles were dug up to 1.50 m in the selected ecosystems and horizon-wise soil samples were collected. All the pedons were classified in the soil order of Ultisols and subclassified as Ustic Palehumult (evergreen forest), Ustic Haplohumult (moist deciduous forest) and Typic Haplustult (rubber plantation), respectively. The soil pH was found to be acidic in all the ecosystems ranging from 4.6 to 5.8. Chlorite, hydroxyl interlayered vermiculite (HIV), mica, kaolinite, feldspars, gibbsite and quartz dominated the mineral assemblages in the clay fractions of soils of natural forest systems. The losses of SiO2 in the non-clay fraction and corresponding enrichment of the component in the clay-sized fraction in all horizons indicated an active continuous weathering process in all the systems of this region. Clay accumulation by way of formation and translocation was highest in the lower horizons of the soils of evergreen (Bt2 at a depth range of 28–57 cm) and moist deciduous (Bt3C at a depth range of 23–150 cm) forest, whereas it was highest at Bt1 at a depth range of 15–28 cm in the plantation soil. The depth variations in the clay formations in natural and manmade forest systems provide insights into ecosystems regulated profile development under natural and man-made systems in the humid tropics, a vital information gap hitherto in soil pedogenesis of the humid tropics. Such pedogenic assessments along with the factors responsible for such modifications would provide important inputs in developing soil health management strategies in the humid tropics.