The archived dataset was collected during a field sampling campaign conducted on Manukan Island, Sabah, Malaysia. A total of twenty-five soil samples were systematically collected from October 2008 to August 2011 across three distinct environmental domains: sandy beach (SB), vegetation-dense (VD), and high-elevation (HE) areas. Topsoil samples (0–50 cm depth) and subsoil samples (100–300 cm depth) were obtained using a hand auger, and additional coral samples from the coastline and sandstone samples (parent geological material) from nearby outcrops were also collected.Soil samples were air-dried, pulverized, and passed through a 2-mm sieve prior to analysis. Physico-chemical parameters, including soil pH, redox potential, and electrical conductivity, were measured using calibrated probes, while soil organic matter content was determined through combustion at 450°C for 12 hours. Particle size distributions were established using the pipette method following pretreatment procedures (carbonate dissolution and organic matter removal). Total concentrations of major elements (Ca, Mg, Na, K) and trace metals (As, Co, Cr, Cd, Ni, Pb, Zn) were quantified by inductively coupled plasma optical emission spectrometry (ICP-OES) after aqua regia digestion. Quality assurance was ensured by employing NIST Certified Reference Material 2711a (Montana II soil), with recovery rates ranging from 90% to 108%.Mineralogical compositions were characterized using X-ray diffraction (XRD), while soil microstructure and physical processes were investigated using scanning electron microscopy (SEM). Major oxide concentrations (SiO₂, TiO₂, Al₂O₃, Fe₂O₃, SrO, SO₃) were determined via X-ray fluorescence (XRF). This dataset provides valuable insights into the biogeochemical processes influencing soil formation, trace metal mobility, and environmental interactions in tropical island ecosystems.