Wheat flour is a hygroscopic product requiring efficient packaging materials to maintain shelf stability and desired quality during long storage periods. This study aimed to assess the effectiveness of four packaging materials (Paper bag, Polypropylene, woven polypropylene bag + Low-density polyethylene, and Purdue Improved Crops Storage) in preserving the physicochemical, microbial, and sensory quality of refined wheat flour over 6 months at room temperature (14.8−26.80 °C). The experiment was conducted under laboratory conditions at the Postharvest Management and Animal Nutrition Laboratory of Jimma University College of Agriculture and Veterinary Medicine. Results revealed that hermetic packaging materials, specifically Purdue Improved Crop Storage (PICS) and Polypropylene bag + low-density Polyethylene (PP + LDPE), were the most effective in maintaining flour quality compared to non-hermetic options such as woven polypropylene bag (PP) and paper bag. As storage duration increased, there was a gradual decline in physicochemical quality, albeit to varying degrees depending on the packaging material. Nutritional losses were significantly lower in hermetic packaging materials. For instance, crude protein losses were 1.82% in PICS and 2.81% in PP + LDPE, compared to 4.64% in woven PP and 3.81% in paper bags. Moisture content increased by 4.43% with PP bags and 3.92% with paper bags, while the slightest changes, 1.99%, and 2.03%, were observed in PICS and PP + LDPE bags, respectively. Additionally, hermetic packaging materials reduced microbial growth. They maintained bulk density, water, and oil absorption capacity, as well as the odor and color of the stored flour compared to non-hermetic packaging materials evaluated. It is recommended that supply chain actors and consumers utilize PICS or PP + LDPE bags to ensure better physicochemical stability, microbial control, and sensory quality of refined wheat flour.