Background The storability and eventual quality of flour is influenced by the optimality of the storage conditions. The present study assessed the effect of storage temperature on extruded composite flour packed in different packages. Methods Oats, soybean, linseed and premix (sugar, salt, Moringa & fenugreek) were blended and extruded. The extruded flour was packed in paper, polyethene and woven polypropylene bags and stored at -18, 25, 35, 45 °C. Moisture content, fat content, water activity, bulk density, aroma, color and microbial load were measured fortnightly for three months. Results The physico-chemical and sensory properties of the flour samples were significantly (p < 0.05) affected by the storage temperature and packaging material along the storage period. The highest moisture content (4.02 g/100g) was recorded on the 90 th day of storage for flour stored in polypropylene bag at -18 °C. The highest water activity (0.68) was recorded from flour packed in woven polypropylene bags stored at 25 °C for 45 days and flour packed in paper bags at days 15 and 45 at 35 °C, whereas the lowest aw (0.18) was recorded for samples stored for 90 days at 45 °C packed in polypropylene bags. Flour samples packed in polyethene bags retained their moisture content. The highest bulk density (0.61 g/ml) was recorded on day 0 and it decreased gradually where the lowest value (0.51 g/ml) was recorded for flour samples packed in polypropylene for 90 days at -18 °C. The highest fat content (9.4g/100g) was recorded at day 0 and it decreased slowly during the storage period where the lowest value (8.2g/100g) was measured from flour samples packed in polypropylene for 90 days at 45 °C. None of the treatments had a microbial load exceeding the standards which could be attributed to extrusion of the food samples. The highest aroma and color liking scores were recorded on the 90 th day of storage for woven polypropylene packed flour at 25 °C and for polyethylene packed flour at -18 °C, respectively. The predicted shelf life was 17 months for samples packed in polyethene and kept at 25 °C and 6.2 months for samples packed in polypropylene and held at 45 °C. Conclusions Woven polypropylene flour bags could be laminated or have a polyethylene liner, so that the flour does not absorb moisture. Shelf stability of the flour can help its successful marketing and distribution.