Food safety in the Nutritional Fulfillment Service Units (SPPG) is influenced by the implementation of workplace hygiene and sanitation. Poor sanitation conditions may promote the presence of flies as mechanical vectors carrying bacteria, thereby increasing the risk of food contamination. This study aimed to describe workplace hygiene and sanitation conditions and the presence of bacteria on flies in SPPGs in Manado City. This study employed a quantitative descriptive design with a cross-sectional approach. Workplace hygiene and sanitation were assessed using an observation checklist based on the Indonesian Minister of Health Regulation (Permenkes) No. 2 of 2023. Fly samples were collected using fly traps and identified through isolation on MacConkey Agar, followed by Polymerase Chain Reaction (PCR), 16S rRNA gene sequencing, and BLAST analysis. The results showed that the hygiene and sanitation compliance rates were 86.7% at SPPG X and 90.0% at SPPG Y. Gram-negative bacterial growth was detected only in fly samples collected from SPPG Y. BLASTN analysis based on 16S rRNA gene sequences revealed that the isolates exhibited 100% sequence identity with the species complexes Klebsiella pneumoniae/Klebsiella variicola and Providencia rettgeri/Providencia hangzhouensis. In conclusion, the hygiene and sanitation conditions at both SPPGs met most of the required standards, although several aspects still require improvement. The presence of Gram-negative bacteria on flies indicates that flies have the potential to act as mechanical vectors carrying bacteria within food processing environments