This work used experimental methods to evaluate the chemical composition of GC-MS, HPTLC-based bioautographaphy, antioxidant, anti-diabetic, and protein denaturation properties of the Neptunia prostrata Linn (family: Mimosaceae) whole plant and leaves. Three methods, namely DPPH, metal chelating, and reducing power assays, were used to estimate the antioxidant effects. In addition, α-amylase, a carbohydrate-hydrolyzing enzyme, was targeted to test the anti-diabetic activity. The protein denaturation assay was used to evaluate the anti-inflammatory activity of the plant. GC-MS, an important analytical tool, was performed to identify bioactive compounds of medicinal plants used in pharmaceutical industries. Biochemical derivatization HPTLC-based bioautography with DPPH was executed to identify antioxidant agents from N. prostrata. The validated HPTLC method was used to quantify identified antioxidant agents. The stability of compounds, preparation of calibration curves, linearity, range, precision, limit of detection, limit of quantification, robustness, and accuracy are examined to develop a robust method. Higher total phenolic content (TPC) content was observed in N. prostrata hydroalcoholic extract of the whole plant (81.12 ± 4.19 mg GAE/g) and methanolic extract of leaves (105.16 ± 3.11 mg GAE/g). Methanolic extract of N. prostrata leaves showed significantly high antioxidant potential for all DPPH (IC50:28.05 ± 1.78 µg/mL), metal chelating (IC50:1598 ± 23.51 µg/mL), and reducing power assay compared to standard ascorbic acid (DPPH assay: IC50:24.14 ± 2.34 µg/mL and metal chelating: IC50:1301.16 ± 6.14 µg/mL). N. prostrata aqueous extract of the whole plant (IC50:179.47 ± 10.59 µg/mL) and leaves (IC50:130.86 ± 3.58 µg/mL) showed significantly high α-amylase inhibitory activity as compared to standard acarbose (IC50:148.62 ± 7.84 µg/mL). Methanolic extract of whole plants (IC50:131.46 ± 11.81 µg/mL) and chloroform extract of leaves (IC50:122.61 ± 8.19 µg/mL) exhibited strong anti-inflammatory activity as compared to standard acetylsalicylic acid (IC50:117.77 ± 4.95 µg/mL). GC-MS analysis revealed the presence of several bioactive compounds, where 2-cyclopenten-1-one, 2-hydroxy showed the most abundant bioactive compounds in the plant with 17.01%. HPTLC-bioautography identified three phenolic acids (chlorogenic acid, gallic acid, and 4-hydroxybenzoic acid) and one flavonoid (naringenin), further quantified with the validated HPTLC method. These findings propose that N. prostrata has therapeutic potential for treating diseases related to oxidative damage, diabetes, and inflammation, which may be due to the presence of bioactive compounds.