Abstract Safe storage guidelines are needed for all common grains at expected moisture contents and temperatures during storage. This would give information to the farmers for scheduling different post-harvest treatments before any quantity and quality loss of the grain. The present study aimed to investigate the effect of storage temperature, seed moisture content and storage period on biochemical, microbial, and physical changes in the pinto beans at several moisture contents: 12, 14, 16, 18, and 20% (wet basis) at different storage temperatures: 10, 20, 30, and 40 °C for 16 weeks of storage, and to develop the safe storage guidelines. All the storage variables (moisture content of the sample, storage temperature, and time of storage) had significant (α = 0.05) effect on the germination, free fatty acid value (FAV), and colour values. There was significant decrease in germination for higher moisture content (16, 18, and 20% w.b.) samples stored at 20, 30, and 40 °C with the increase in storage period along with an increase in FAV and had significant colour change. Aspergillus glaucus group was the predominant microflora found in the beans irrespective of the storage temperature, and Penicillium spp. were also common along with A. glaucus group at lower storage temperatures (10 and 20 °C). Pinto beans with lower initial moisture contents (12 and 14% w.b.) can be stored safely at lower temperatures (10 and 20 °C) maintaining appreciable seed germination, seed coat colour, and microbial stability for 16 weeks. The pinto beans at higher moisture contents (16, 18, and 20% w.b.) must be dried to lower levels before 8, 5, and 3 weeks, respectively for prolonged storage.