Blossom-end enlargement (BEE) is a physiological disorder in cucumbers (Cucumis sativus L.) that affects postharvest quality and results in commercial loss due to reduced product value. Pre-cooling using modified atmosphere packaging (MAP) has been encouraged as a preventive method of BEE; however, BEE can still be observed under actual distribution conditions. This study reexamined the process from harvesting in midsummer to arriving at the market (550 km) and storage, while considering the impact of packaging materials, packaging methods, and human factors on BEE occurrence. More than 18 h were required from harvest to delivery at the pre-cooling warehouse at the common shipping site; however, despite using a refrigerated truck, the temperature inside the packaging increased again during transportation. The temperature then dropped during 24 h of pre-cooling; however, it did not reach 10 °C, the appropriate storage temperature for cucumbers. MAP suppressed the occurrence of BEE compared to conventional film packaging; however, the BEE index varied greatly between individuals who performed the packaging. We determined that tying both ends of the packaging film increases the degree of airtightness as individual differences decrease and is more effective at suppressing BEE. Porous mineral-containing film (PM) packaging, which generates a modified atmosphere (MA), significantly suppressed BEE compared to conventional perforated film (C). In 2019 transport trials, the BEE index at 6 DAH for C film was 77.3, while for PM film it was only 12.0. Furthermore, we found that the effectiveness of PM film was significantly affected by human-related operational factors. The novel packaging method of tying both ends of the film (PM-T) provided the most consistent BEE suppression and lowest BEE index regardless of the packaging worker, demonstrating its superior potential in standardizing airtightness and minimizing human-related operational variability.