The nutritional and microbiological qualities of pumpkin (Cucurbita pepo) seed composite flours were studied using standard nutrient assessment and microbiological methods. Proximate and nutrient content analysis showed that pumpkin (Cucurbita pepo) seed flour (PSF) had low moisture (6.48 ±0.72%) and starch content (19.75 ±2.47%) with high ash (5.92 ±0.81%), fat (33.12 ±2.20%), fibre (7.24 ±0.64%) and protein (27.05 ±2.01%) contents over wheat flour (WF1). Mineral and peroxide values were high in pumpkin seed flour (PSF) than wheat flour (WF1). The blended flours (CF1-CF6) recorded higher mineral (mg/100 g) and peroxide (meg/kg) contents than wheat flour (WF1) - the control; with CF6 (60% pumpkin) having the highest values (Ca-95.40±1.63, K-688.40±2.91, Fe-6.76±0.05, Zn-10.61±1.06 and peroxide - 3.24±0.02). Bacterial and fungal counts (CFU/g) of blended flours ranged from 2.83x103 ±0.09- 3.15x103 ±0.52 and 3.59x102 ±1.81- 3.92x102 ±1.12 respectively. WF1 flour recorded the highest bacterial and fungal counts while CF6 recorded the least bacterial and fungal counts. Four (4) bacterial and three (3) fungal isolates were identified to include Bacillus species, Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, and Penicillium species, Mucor species, Aspergillus species respectively. Due to the high nutritional contents and reduced microbial counts of the blends, inclusion of pumpkin seed flour in supplemented products should be encouraged so as to enhance nutritional requirements and eradicate malnutrition among individuals especially infants and children.