Injera is an important staple food in Ethiopia and mostly it is made from Teff and other crops in small amount such as corn, rice, and wheat. However, post-manufacturing contamination and improper storage make them extremely susceptible to microbial spoilage. The spread of mold on injera and baked foods is a concern, leading to financial loss and consumer dissatisfaction. Adding organic acid salts to the process as a preservative is the main way to prevent this problem. However, it have drawbacks. Other methods can be used to extend the shelf life of the product. The aim of this study was to prolong the shelf life of injera by controlling temperature and relative humidity to form a regulated atmosphere. This may be possible by using an evaporative cooler from a locally available clay pot. It was designed, manufactured, and tested for Injera storage in Bahir Dar, Ethiopia. This system is an economical and efficient way to lower the temperature and increase relative humidity. The performance of the cooler was evaluated in terms of temperature drop and evaporation efficiency. The results show that the evaporative cooler with load of injera can reduce the daily maximum ambient temperature from 28.98 °C to 22.90 °C. The temperature drop of up to 6.08 °C and the relative humidity can rise from 28.78% to 80.94% in the storage room and are evaluated for injera storage. This study also identified the types of spoiled injera fungi species. Isolates were identified based on colonial and microscopic characteristics. Three fungal genus Penicillium sp., Aspergillus sp., and Rhizopus sp. The effects of temperature, relative humidity, and pH were studied for the optimization of evaporative coolers identified from rotten injera and designed for injera storage. The evaporative cooler can store freshly made injera for 9 days before any visible mold stains appear, significantly reducing weight loss with an average cooling efficiency of 79.31%.