The nutritional, phytochemical, and antimicrobial attributes were determined for kernels (shelled) and seeds of five different cultivars of pumpkin, namely Kashi Harit (KH), Narendra Upkar (NU), Pusa Vishwas (PV), Narendra Agrim (NA), and Azad Pumpkin 1 (AP1), that are grown in subtropical regions of India. Seeds and kernels of the KH cultivar showed the highest values for fat, ash, protein, and minerals such as P, Mg, Mo, Mn, Fe, Cu, Zn, and Se. Among the cultivars, the KH cultivar also showed good antioxidant properties for both seeds and kernels. The tocopherols (α, β+γ) and phytosterols (β‐sitosterol and stigmasterol) content were abundantly found in the seeds and kernels of KH and AP1 cultivars. Seeds of all the cultivars scored higher values for antinutritional compounds such as oxalate, cyanide, tannin, and phytate than their kernels. The squalene content ranged from 82.19 to 86.91 mg/100 g in seeds and 69.94–77.42 mg/100 g in kernels of different cultivars. β‐carotene was found predominantly in seeds of the AP1 cultivar (7.33 μg/g) and kernels of the KH cultivar (5.58 μg/g). LC‐ESI‐MS analysis of seed extract revealed that protocatechuic acid, ferulic acid, p‐coumaric acid, chlorogenic acid, vanillin, quercetin, myricetin, kaempferol, and luteolin were the major phenolic compounds present in the pumpkin seed extract. The disk diffusion method was used for antimicrobial screening of seeds and kernels of the KH cultivar. A clear zone of inhibition was found with all selected bacterial strains Staphylococcus aureus, Escherichia coli, Enterococcus faecalis, Bacillus subtilis, Salmonella typhi, and fungal strains Candida albican and Aspergillus niger.