In this study, we investigated the effects of several pre- and postharvest factors on Braeburn browning disorder (BBD) incidence using a nine-factor experimental design. The design allowed the determination of the effects of single factors as well as their interaction with growing season and storage time. Flesh browning in Braeburn increased in severity with storage duration. BBD incidence was reduced with calcium and potassium fertilizers application, while it was increased when triazoles were used. Delayed controlled atmosphere application resulted in less browning in storage, while treatment with 1-MCP increased BBD incidence. More browning was observed in fruit stored at above optimal CO2 levels. BBD incidence was increased when the concentration of O2 in CA was increased from 1 kPa to 3 kPa (optimum CA) or 6 kPa. Finally, the various factors showed a different effect for different growing seasons and storage time. These findings suggest a possible mechanism for the development of BBD. Further work should focus on extending the experimental design to include the interactions between the different pre- and postharvest factors.