Winter melon fruits were grown in the field using anaerobic soil disinfestation (ASD) and conventional fertilizer alone as the control treatment. Fruits were harvested and stored at 20 °C for 120 d, the juice was processed on day one and day 120, and the effects of soil amendment and 120 d storage on the juice’s physical and chemical (sugars, acids, volatile and nutritional compounds) properties were evaluated. Fruit juice extracted from ASD-grown fruit had greater magnitude of zeta potential than the control juice, indicating it was physically more stable than the juice obtained from the control conditions. ASD fruit juice had lower soluble solids content (SSC), and lower volatile compounds that contribute green, grass, and sulfur notes, and negatively influence flavor quality. ASD fruit juice had higher vitamin B5 and cytidine. Juice processed from 120 d stored fruit had less yield due to 12.4–15.6% weight loss. The non-soluble solids content was higher and particle size was larger, and the SSC and individual sugars decreased. However, titratable acidity (TA) increased primarily due to increased citric acid. Out of 16 free amino acids, 6 increased and only 1 decreased. However, three out of five nucleosides decreased; vitamins B1 and B6 increased; vitamins B2, B3 and C decreased. Overall, juice derived from fruit produced using ASD was physically more stable and had less SSC and off-odor volatiles than the control, while the fruit juice of those stored for 120 d had lower SSC and higher TA and nutritional profiles, comparable to freshly harvested fruit.