Zebrafish (Danio rerio) is one of the top model organisms used in biomedical research. Therefore, it is fundamental that zebrafish facilities continuously improve husbandry methods to provide fish with the best physiological and welfare conditions that suit each experimental purpose. Nutrition is a husbandry aspect that needs further optimization, as it greatly affects growth, reproduction, health and behaviour. Here, we have compared the impact of different feeding regimens on zebrafish survival, growth and reproductive performance. Mutant and wild-type zebrafish were raised using several combinations of two cold-extruded processed feeds—Skretting^®GemmaMicro and Sparos^®Zebrafeed—and one live feed (rotifers). Zebrafeed^® outperformed GemmaMicro^® in terms of survival rate, and embryo viability was also higher when the spawners were fed with Zebrafeed^® either from larval stage or upon sexual maturation. In contrast, GemmaMicro^® favoured growth, both in size and weight. The use of rotifers until 60 days post-fertilization improved survival of fish co-fed with GemmaMicro^®, while delaying their growth. Zebrafeed^® performance was not affected by co-feeding rotifers. Overall, we showed that different nutritional formulas affect physiological parameters, allowing for the establishment of feeding protocols adapted to the objectives of each facility. At the same time, we validated Skretting^®GemmaMicro and Sparos^®Zebrafeed as two commercially available feeds that are well suited for zebrafish nutrition in a laboratory environment.