While γ-aminobutyric acid (GABA) promotes nutrient accumulation in green microalgae, its effects on marine diatoms—critical aquaculture feed—remain understudied. Understanding the physiological response of diatoms to exogenous GABA is vital for optimizing high-quality feed production. In this study, we investigated the impact of GABA on diatom growth, photosynthetic performance, proximate composition (lipids, proteins, carbohydrates, and fatty acids), and oxidative stress markers of two commonly used feed diatoms Phaeodactylum tricornutum and Chaetoceros muelleri. GABA effects were species-specific: low doses (0.2–1.0 pmol cell^-1) inhibited P. tricornutum at the exponential onset, while C. muelleri remained resilient to higher doses (1.5–16.2 pmol cell^-1). Notably, this resilience in C. muelleri shifted to growth promotion when GABA was applied at the late stage, demonstrating clear stage-dependency. In P. tricornutum, supplementation with 0.2–1.0 pmol cell^-1 GABA triggered a significant accumulation of cellular carbohydrates, proteins, and lipids accompanied by a broad-spectrum increase in various cellular fatty acid concentrations including polyunsaturated fatty acids (PUFAs), such as eicosapentaenoic acid and docosahexaenoic acid, important PUFAs. Notably, 1.0 pmol cell^-1 GABA induced a three-fold increase in carbohydrate and lipid levels over the control. GABA triggered significant oxidative stress and photosynthetic inhibition in P. tricornutum in a dose-dependent manner, while C. muelleri exhibited high physiological tolerance with no marked changes in reactive oxygen species and superoxide dismutase or photosynthetic efficiency. A two-stage cultivation strategy involving initial biomass maximization and subsequent GABA-induced nutrient enrichment can be effectively utilized to bio-fortify P. tricornutum for use as aquaculture feed.