This study aimed to investigate the effectiveness of dimethyl dicarbonate (DMDC) at various concentrations (0–250 ppm) in inhibiting the growth of Escherichia coli TISTR 117 and spoilage microbes in passion fruit juice (PFJ) and its impact on the physicochemical and antioxidant quality of the juice during refrigerated storage. The highest log reduction in the total viable count, yeast/molds and E. coli was attained in PFJ samples with 250 ppm of DMDC (p ≤ 0.05) added. Microbial growth inhibition by DMDC followed the first-order kinetic model with a coefficient of determination (R2) and inhibition constants (k) ranging from 0.98 to 0.99 and 0.022 to 0.042, respectively. DMDC at 0–250 ppm showed an insignificant effect on pH, °Brix, color (L*, a*, b*), ascorbic acid, total phenolic compound (TPC), total flavonoid content, and antioxidant activity (DPPH, FRAP) (p > 0.05). Control (untreated PFJ), DMDC-250 ppm, and pasteurized (15 s at 72 °C) samples were subjected to 27 days of cold storage at 4 °C. A decreasing trend in pH, total soluble solid, ascorbic acid content, DPPH and FRAP values were observed in all the samples during refrigerated storage. However, the DMDC-250 ppm sample showed a better prospect in physicochemical quality changes compared to the pasteurized and untreated control PFJ samples. ΔE values showed marked changes in the control sample than the DMDC-250 ppm and pasteurized samples at 27 days of storage. Additionally, the total viable count and yeast/mold count were augmented during storage, and an estimated shelf-life of the control, DMDC-250 ppm, and pasteurized samples was approximately 3, 24 and 18 days, respectively. In conclusion, DMDC at 250 ppm could ensure microbial safety without affecting the quality attributes of PFJ during 24 days of storage at 4 °C.