The pigeon pea (Cajanus cajan (L.) Millsp.) is one of the major grain legume crops of the tropical world and recent evidence indicates that it possesses various health benefits. However, to the best of our knowledge, no comparison has been made on the nutritional composition and biological functions of its leaves, seeds, and roots. Therefore, the present study investigates which part of the C. cajan (L.) Millsp plant has the highest potential for development as a health food product. Results show that C. cajan (L.) Millsp roots (CCR) have a higher total polyphenol content (TPC) and total flavonoids flavonoid (TFC) contents than leaves and seeds. The antioxidant, anti-hyperglycemic, and anti-bacterial activities of CCR extracted with hot water (HWCR), 50% ethanol (EECR50), and 95% ethanol (EECR95) were determined. We found that EECR95 had the strongest antioxidant activity, as evaluated by 1,1-Diphenyl-2-picrylhydrazyl radical (DPPH) and 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS+) scavenging, and reducing power. EECR95 exhibited higher anti-hyperglycemic ability (inhibition of α-glucosidase and α-amylase activities) and anti-glycation effects (IC50 = 39, 120 and 229 μg/mL, respectively) than HWCR and EECR50. EECR95 also exhibited potent anti-bacterial activities on E. coli, Staphylococcus aureus, Porphyromonas gingivalis, and Streptococcus mutans, with minimum inhibitory concentrations of 113, 180, 16, and 100 μg/mL, respectively. Based on above results, we conclude that CCR has considerable potential for health food development and further studies of CCR in animals to confirm these biological effects and safety issues are warranted.