Abstract: To promote sustainable aquaculture, plant-based ingredients are increasingly replacing fish meal (FM) and fish oil (FO) in aquafeeds, altering broodstock diets and reducing omega-3 long-chain polyunsaturated fatty acids (ω-3 LC-PUFAs), essential for reproductive success and progeny growth. Despite the critical role of ω-3 LC-PUFAs, particularly docosahexaenoic acid (DHA) in brain function, data on how fry cope with FM/FO-free diets during early development remain limited. To address this, we conducted a 2-year experiment comparing three broodstock diets: a commercial diet (C diet), a total plant-based diet (V1 diet), and a plant-based diet supplemented with DHA-rich Schizochytrium sp. microalgae oil (V2 diet). After reproduction, progeny were fed either a C diet or a plant-based diet (V). Six groups (C–C, C–V, V1–C, V1–V, V2–C, V2–V) were analyzed for survival, feed intake, and growth, as well as neuropeptide, neurotransmitter, and intestinal hormone expression. Results showed enhanced robustness in fry-fed V diets, particularly from V1 and V2-fed broodstock, with improved survival and feed intake. Fry from DHA-supplemented broodstock (V2–V) compensated for initial growth delays, achieving growth comparable to fry from commercial-fed mothers (C–V) within 30 days. Neurophysiological and gut–brain adaptations revealed complex compensatory mechanisms enabling fish to thrive on sustainable diets. These findings highlight the potential of DHA supplementation in plant-based diets to support sustainable aquaculture and warrant further validation under diverse nutritional and environmental conditions.