Milk powder is one of the most traded dairy products globally, largely being used to manufacture commercially sterilized products. Skim milk powder is frequently contaminated with spores of Bacillus species and carried over from raw milk due to their ability to survive processing conditions. Our previous study proved that it is possible to use optimized raw milk holding conditions to keep their population low, which may help in making low spore count powder. This pilot scale trial was conducted to produce low spore count powder by controlling the raw milk holding conditions, to keep the spore populations low. Bacillus licheniformis being a predominant spore former in milk powders was used as an inoculant for the challenge study. Inoculated raw milk samples (batches of 1500 lbs each) were held at optimized storage conditions T1 (4°C for 24 h) and T2 (8°C for 72 h). The PMO based storage conditions (10°C for 4 h followed by 7°C for 72 h) were kept as a control, before producing skim milk powder. Samples were drawn at different stages pre- and post-storage, pasteurization (73°C for 15 s), evaporation, and spray drying (outlet and inlet temperature of 200 and 95°C, respectively), and analyzed for sporeformers using standard culturing methods. Spore counts were done by heating the samples at 80°C for 12 min, before plating on Brain Heart Infusion agar. All samples were analyzed in the replicates of 3, and means were compared using ANOVA. Treatment T1 and T2 log spore counts (1.79 ± 0.03 and 1.82 ± 0.04, respectively), were significantly lower than control (2.59 ± 0.05), after raw milk storage step. Similarly, sporeformers log counts for T1 (3.84 ± 0.02) were significantly lower than T2 (4.07 ± 0.08) and control (4.13 ± 0.04). Skim milk powders prepared using optimized storage conditions T1 showed significantly (P < 0.05) lower spore and sporeformer counts (0.58 ± 0.04 and 1.82 ± 0.05 log cfu/g), as compared with T2 (0.86 ± 0.16 and 1.90 ± 0.03) respectively, and control (1.03 ± 0.06 and 2.74 ± 0.03, respectively). This shows that skim milk powders with reduced counts can be prepared by just optimizing raw milk holding conditions.