The production of genetic sexing strains (GSS) of tephritid flies for sterile insect technique (SIT) programs convey the need to determine new conditions for packing and shipment since these flies are more susceptible to stressors than standard bisexual strains. We studied the effect of hypoxia, pupae size, and temperature on the new GSS Tapachula-7 of Anastrepha ludens flies (Diptera: Tephritidae). In one experiment, we tested the interaction size hypoxia using three pupae sizes, 6 (11.6 ± 1.1 mg), 7 (15.3 ± 1.5 mg), and 8 (17.9 ± 1.3 mg) (95% of produced pupae exhibit these categories of size), and four hypoxia periods, 12, 24, 36, 48 h and a control. In a second experiment, we tested two periods of hypoxia (24 and 48 h) and four temperatures: 15, 20, 25, and 30°C and a control (without hypoxia at laboratory temperature). Our results showed that the emergence and percent of fliers from the pupae exposed to hypoxia were adversely affected; however, emergence was higher in pupae of size 7. Treatment for 12 and 24 h hypoxia led to a higher number of fliers. In the case of the interaction of hypoxia and temperature, it was observed that those flies that emerged from the pupae exposed to hypoxia at 15 and 20°C exhibited quality control parameters similar to those that were not exposed to hypoxia. We discuss our results on the basis of the metabolic response to these factors and its application in the SIT programs.