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Fungal endophytes establish an important niche within the host plant through the secretion of chemical constituents. Isolation of bioactive metabolites could be a vital source for inhibiting the function of enzymes such as alpha-glucosidase and urease. The present study aimed to elucidate the potential of endophytes associated with Boswellia sacra through bioassay-guided isolation and identification of secondary metabolites with enzyme inhibitory ability. Endophytic fungal strains viz. Penicillium citrinum, P. spinulosum, Fusarium oxysporum, Alternaria alternata and Aspergillus caespitosus were identified through genomic DNA extraction, PCR amplification, sequencing and phylogenetic analysis. The enzymes inhibition analysis of the ethyl acetate extract from pure cultures suggested that P. citrinum possess significantly higher enzyme inhibitory activities compared to other strains. The active strain was subjected to chromatographic isolation and nuclear magnetic resonance methods to identify bioactive compounds. The bioactive extracts resulted in the isolation of 11-oxoursonic acid benzyl ester (1), n-nonane (2), 3-decene-1-ol (3), 2-Hydroxyphenyl acetic acid (4), and Glochidacuminosides A (5). Among pure compound, 11-oxoursonic acid benzyl ester (1) showed significantly higher enzyme inhibition activity compared to other metabolites. Our results suggest that the endophytic microorganism associated with the arid-land tree can offer a rich source of biologically active chemical constituents that could help discover lead drugs for enzyme inhibition.