Rapid degradation of fresh‐cut papaya limits its marketability. Hydrothermal treatments in combination with a calcium dip, applied to whole fruit before slicing, and also the application of chitosan as a coating film, have been found to have very good results in maintaining the quality of fresh‐cut fruits. Based on these considerations, the aim of this study was to evaluate the effect of hydrothermal treatment (HT; 49 °C, 25 min) containing calcium chloride (Ca; 1%, w/v) followed by dipping in chitosan (Chit; 1%, w/v, 3 min) on the physical, chemical, and microbial qualities of papaya slices stored at 5 °C for 10 d. Pulp color, firmness, ascorbic acid, total phenolics, β‐carotene, and lycopene were evaluated every 2 d while the microbial quality (mesophilics, psychrophilics, molds, and yeasts) was evaluated every 5 d. Fruit treated with HT‐Ca and HT‐Ca + Chit showed better color and firmness retention than Control and Chit. Papaya slices treated with HT‐Ca + Chit had higher nutritional content and lower microbial growth at the end of storage. The application of the HT‐Ca + Chit could be used to reduce deterioration processes, maintaining physical, chemical, and microbial qualities and increasing the shelf life of fresh‐cut papaya stored at 5 °C. Practical Application The application of hydrothermal‐calcium chloride, combined with chitosan coatings, reduced deterioration processes and presented antimicrobial activity, thus increasing the shelf life and showing its potential use in food preservation. Also, it can constitute an alternative for the natural preservation of fresh‐cut papaya for which the use of synthetic chemicals is objectionable.