Wheat flour is a global staple food commodity, yet its microbiological and chemical safety remains a public health concern due to potential contamination throughout the production and supply chain. This study provides a preliminary baseline assessment of the quality and safety of 14 commercial wheat flour samples (X1–X14) obtained from markets in Jeddah, Saudi Arabia. Standard microbiological methods were employed to detect pathogenic indicators. Heavy metal concentrations were quantified. Ochratoxin-A and total aflatoxins (B1 + B2 + G1 + G2) were analyzed, while pesticide residues were determined. A total of 23 bacterial isolates were purified and identified via 16S rRNA gene Sanger sequencing, with phylogenetic trees constructed using MEGA12, and hemolytic activity was assessed on sheep blood agar. All samples were negative for Salmonella spp., Staphylococcus aureus (S. aureus), Bacillus cereus (B. cereus), and Escherichia coli (E. coli) were below 10 CFU/g, indicating compliance with international safety standards. However, yeast and mold counts varied significantly, with one sample (X8) exhibiting a critically high count (830 CFU/g). Heavy metal levels were generally within Codex Alimentarius limits, though one sample contained elevated lead (0.566 mg/kg). Ochratoxin-A was detected in Three samples (X1: 0.17 μg/kg; X2: 0.12 μg/kg; X9: 0.14 μg/kg), while total aflatoxins were absent from all samples. The most prevalent pesticide residue was deltamethrin (X2, X3, X4, X6; range 0.015–0.059 mg/kg), followed by chlorpyrifos ethyl (X3: 0.009 mg/kg; X6: 0.008 mg/kg). Molecular identification revealed a taxonomically diverse bacterial community dominated by the genus Staphylococcus (13/23 isolates, 56.5%), followed by Rothia kristinae (3/23), Bacillus paramycoides (2/23), Peribacillus frigoritolerans (1/23), and other genera (4/23). Hemolytic activity testing revealed that all staphylococcal isolates were gamma-hemolytic (non-hemolytic), whereas the three Bacillus isolates (Bacillus paramycoides and Peribacillus frigoritolerans) exhibited beta-hemolysis. These preliminary findings underscore the necessity for routine monitoring of post-harvest handling, storage conditions, and pesticide residues to ensure consumer safety. Due to the limited sample size (n = 14), future studies with broader geographic and seasonal coverage are recommended.