In this study, different parameters including phytochemical, nutritional, anti-nutritional compositions, and endophytic microbial populations that can play roles in the health benefits of tiger nut (Cyperus esculentus L.) tubers were determined in tiger nut tuber samples obtained from three different local markets situated in Osogbo, Ile-Ife, and Ado-Ekiti in the Southwestern part of Nigeria. Tannins (127.33-620.1 GAE/100 g), alkaloids (0.5-18%), flavonoids (4.5-9.5%), terpenoid, and cardiac glycoside were present in all the samples. The most and least abundant elements in the tiger nuts were Potassium (0.255-0.345%) and Copper (0.0007-0.0009%), respectively. The anti-nutrients found in the tiger nut tubers were oxalate (0.42-1.08 mg/100 g), tannin (0.42-0.98 mg/100 g), and phytic acid (0.56-1.64%). By molecular techniques, Lactococcus lactis, Bacillus cereus, Enterobacter cloacae, Bacillus licheniformis, Bacillus aryabhattai, and Enterobacter roggenkampii were identified as the endophytic bacteria in the tiger nut tubers, while the endophytic fungi isolated were Saccharomyces cerevisiae and Candida tropicalis. The presence of reportedly pharmacologically active phytochemicals, essential elements, endophytic bacterial and fungal strains with probiotic potentials, and negligible amounts of anti-nutrients in the study tiger nut samples supports the nutritional and health benefits of tiger nut tubers.