To expand the availability of marketable eyed eggs, a common practice in rainbow trout aquaculture is to store eyed eggs at low temperatures (2–4 °C) for periods of up to 2–3 weeks. Early exposure to environmental stimuli such as temperature can impact fish physiology, growth, metabolism, and nutrition at mid- or long-term questioning about the potential effects of such breeder practice. This study aimed to test the impact of incubating eyed eggs at low temperatures (3 °C instead of 12 °C) for 15 days on resistance to later stresses using two experimental rainbow trout lines divergent for fat content. Plasma parameters (i.e. cortisol, glucose, lactate, and chloride ions) have been measured after an acute confinement challenge. For the hyperthermia challenge, time at the loss of equilibrium was compared between lines and incubation temperatures. Our results showed that deformities rate and early survival were not affected by cold temperature storage. Furthermore, plasma parameters measured after the confinement were not impacted by temperature. The two lines differently responded to the hyperthermia challenges with the fat line showing significantly higher resistance to temperature elevation. These findings suggest that the incubation temperature did not impair the responses to stress at the juvenile stage, indicating that the practice of cold storage of eyed eggs does not appear to be detrimental to subsequent rearing.