The present study evaluated the nutritional value and antimicrobial activities of Thalassiosira weissflogii and Tetraselmis sp. concentrates. The study also ascertained the effect of microalgae supplemented diets on the growth and survival of Penaeus vannamei post larvae (PL 18, mean weight: 19.714 ± 1.62 mg). Microalgae concentrates were prepared by flocculation, and the proximate composition showed no significant difference in the crude protein content between these species (T. wesissflogii: 43.07 ± 1.78%; Tetraselmis sp. 42.11 ± 2.55%; p > 0.05). However, the crude lipid content of T. weissflogii was significantly (p < 0.05) higher (20.11 ± 1.02%) than that of Tetraselmis sp. (10.56 ± 0.27%). Significantly higher (p < 0.05) polyunsaturated fatty acid was found in Tetraselmis sp. compared to T. weissflogii. Significantly higher inhibition against Vibrio parahaemolyticus was shown by the Tetraselmis extract compared to that of T. weissflogii. Further, a 42-day feeding trial was conducted with three different inclusions of T. weissflogii (THA) and Tetraselmis sp. (TET) concentrates in P. vannamei nursery diet (0, 0.5, 1, and 1.5 g kg−1 of diet). Significantly higher (p < 0.05) average body weight (ABW) was observed in TET0.5, TET1.0, TET1.5, THA1.0 and THA1.5 compared to the control. The highest ABW was recorded in TET1.0 (0.96 ± 0.02 g), which was significantly higher than all other treatments. Significantly higher (p < 0.05) weight gain was observed in TET1.0 (0.94 ± 0.02 g) compared to the rest of the diets. Significantly higher (p < 0.05) average daily gain was observed in TET1.0 (22.48 ± 0.55 mg day−1). Haematological parameters of P. vannamei fed with microalgae concentrates were higher than those of the control group. The gut microbial analysis showed a significant reduction in total Vibrio count in the animals fed with 1% and 1.5% Tetraselmis or Thalassiosira compared to other treatments. These results indicated the beneficial effect of growth and better antimicrobial property to withstand against the common pathogenic microbe and thus indicating the beneficial effect in the early life stages of shrimp.