Postharvest physiological deterioration (PPD) of fresh cassava roots limits their shelf-life to about 48 h. There is a demand for simple, cheap, and logistically feasible solutions for extending the shelf life of fresh cassava roots in industrial processes. In this study, three different types of bag materials were tested, namely woven polypropylene, tarpaulin, and jute as a potential storage solution for cassava roots with different levels of mechanical damage. Microclimate related to temperature, humidity, and carbon di-oxide (CO2) was monitored in order to understand the storage conditions for up to 12 days. The results showed that fresh cassava roots could be stored for 8 days, with minimal PPD and starch loss (2.4%). However, roots with significant mechanical damage in the form of cuts and breakages had a considerably shorter shelf life in the storage bag, compared to whole roots and roots with retained stalk (peduncle) where roots are connected to the main plant. Wetting of the roots and bag material were not significant factors in determining the shelf life and starch loss. Carbon dioxide concentration in the stores was significantly correlated with the starch loss in fresh cassava roots and is proposed as a possible method for continuously and remotely monitoring starch loss in large-scale commercial operations and reducing postharvest losses.