Aims: A study on biosorption ability using encapsulated endophytic fungi has been carried out to investigate its biosorption potential in removing heavy metals. Biosorption has emerged as an alternative bioremediation process to remove and sequester heavy metal ions from polluted water. An endophytic Pestalotiopsis sp. (isolated from Nypa fruticans) was found to be able to resist copper (Cu), chromium (Cr), lead (Pb) and zinc (Zn) up to 1,000 ppm and thus the aim of this study was to investigate the biosorption ability using encapsulated live and dead Pestalotiopsis sp. biomass (at pH 4-6) to remove heavy metals. Additionally, a proteomic study was conducted to investigate down- and up-regulation expression levels of proteins under the treatment of the heavy metals. Methodology and results: Encapsulated live fungal biomass displayed higher efficiency in removing chromium at pH 5 and 6, while both encapsulated live and dead biomass were able to remove lead at pH 4 and 5 and copper at pH 5. Five (5) proteins of interest were identified via MALDI-ToF analysis. Among the proteins identified, multidrug resistance protein (MRP homolog) was up-regulated in the presence of lead. Conclusion, significance and impact of study The data obtained in this study provides an initial understanding of the biosorptive and defensive mechanisms of Pestalotiopsis sp. under heavy metal stress.