Cold treatment and fumigation are widely applied approaches to disinfest storage pests after harvest of fruits, nuts, grains, and vegetables. Cold conditions can limit the development and survival of spotted-wing drosophila, Drosophila suzukii Matsumura, in fruit and fumigation of blueberries with SO2 may control blueberry maggot, Rhagoletis mendax Curran. In this study, we found that at least 21 d of 0.5 °C was needed for achieving 98.3% reduction in R. mendax making this unsuitable for pre-export disinfestation. The average concentration of SO2 in modified atmosphere packages with slow release SO2 pads was only 2.93 ( ± 0.37) µL L−1 held at 0.5 °C, too low for control of R. mendax. To develop a fruit treatment schedule that controls both pests, we first combined fumigation of 10,000 µL L−1 SO2 and CO2 at 6% v/v for 30 min followed by cold storage at 2 °C for 12 d or − 0.5 °C for 6 d to mimic shipping conditions. With short fumigation and long cold, R. mendax survival was reduced by no more than 4%, whereas D. suzukii was controlled effectively by cold in fumigated and non-fumigated conditions. However, fruit condition was negatively affected by SO2, so lower dosages were explored. 300 and 500 µL L−1 of SO2 with a longer exposure duration were applied at room temperature. These dosages successfully controlled R. mendax without damaging fruit quality. Survival of R. mendax to pupation was reduced by 58% and 61% after 2 d and 3 d fumigation at 22 ⁰C with 300 µL L−1 SO2, respectively. Fumigating infested blueberries at 22 °C with 500 µL L−1 of SO2 reduced pupation by 97% after 2 d and by 100% after 3 d. Fruit quality parameters were not significantly reduced by the low SO2 fumigation regimen on three different blueberry cultivars. Our data indicate that both insect pests can be controlled in harvested blueberries without loss of fruit quality by the combination of fumigation for 3 d at 22 ⁰C with 500 µL L−1 SO2, followed by cold storage. These results can inform export protocols for blueberries as part of a systems approach that combines in-field management and postharvest control programs.