Transportation vibration adversely affects fresh produce during transportation. In addition, storage temperature affects the quality of fresh commodities. The physical changes in Java apples during transportation and storage were evaluated in this study. Java apples were transported from local farms to wholesale markets (180 km). Java apples were stored at room temperature (28°C) for six days. Physical qualities such as weight loss and firmness of the Java apple samples were evaluated. The RGB image acquisition system was used to assess changes in the color of the Java apple. The vibration showed that more than 70% of the acceleration occurred between 220-290 cm/s2 in the vertical and horizontal directions during transportation. Analysis showed that physical qualities, such as weight loss and firmness, were strongly affected by the packaging used, vibration during transportation, and storage temperature. The weight loss and reduction in firmness was highest in Java apples transported using wholesaler packaging (packaging A). The lightness, yellowness, and hue values decreased significantly because transportation vibration was relatively high, and the Java apples were stored at room temperature. Redness, total color difference, and color index increased significantly in Java apples that were transported using package A and stored at room temperature. The results showed that the use of transportation packaging affected changes in the physical quality of Java apples. Packaging A generally increase in weight loss, hardness, and changes in fruit color than other packaging types.