Microbiological safety and quality consistency are critical challenges in the production of traditional Indian fried snacks, particularly in small-scale food enterprises. With growing export demand, maintaining strict quality control measures is essential. This study assessed the microbiological and physicochemical quality of five traditional Indian fried snacks—Kerala Murukku, Kerala Mixture, Banana Chips, Tapioca Chips, and Achappam—produced in a Food Safety Management System (FSMS)-certified facility over a four-year period (2020–2023). Products were evaluated for moisture, pH, salt content, acid value, and Total Plate Count (TPC). The number of ingredients for each product was recorded from standardized product formulation documents. TPC levels remained within acceptable limits (below 50,000 CFU/g) across all products. Among them, Kerala Mixture consistently showed the highest microbial counts (up to 4.61 log CFU/g) and Achappam the lowest, with no detectable variance (1.00 log CFU/g). Statistically significant year-wise differences (p < 0.05) were observed in all quality parameters. Kerala Mixture showed variation in salt and microbial load; Kerala Murukku varied in moisture, pH, and salt; while Tapioca Chips varied in moisture and salt. PCA identified that TPC, salt content, number of ingredients, and pH were key contributors to product variability. Cluster analysis confirmed Kerala Mixture as the most susceptible product to contamination risk. These findings provide valuable insights into the quality trends within an FSMS-certified environment and highlight the importance of strict post-processing controls.