The residual antibiotics in livestock excreta (LE) have been regarded as a potential threat to the ecosystem and human society. Some photoautotrophic microalgae, however, were found to metabolize them during active biomass photosynthesis. This study investigates how the strength of the antibiotics impacts the overall biodiesel yield and composition of the harvested microalgal biomass grown from LE. The microalgal growth results demonstrate that increasing the concentration of residual antibiotics suppresses the microalgal growth rate from 0.87 d−1 to 0.34 d−1. This 61% lower biomass production rate supports the proposition that the kinetic impact of antibiotics may slow lipid synthesis. Moreover, the analytical results of fatty acid methyl ester (FAME) demonstrate that amoxicillin substantially reduces the C16:0 content by over 96%. This study evidences that the functional group similarity of amoxicillin may competitively inhibit the esterification reaction by consuming methanol. This explanation further highlights that residual antibiotics interfere with microalgal lipid synthesis and its transesterification. Moreover, it was confirmed that the presence of residual antibiotics may not affect the major nutrient removal (total nitrogen: 74.5~78.0%, total phosphorus: 95.6~96.8%). This indicates that residual antibiotics inhibit the metabolism associated with carbon rather than those associated with nitrogen and phosphorus, which is connected to the decrease in the biodiesel yield. Overall, these results reveal that the frequent abuse of antibiotics in livestock may harm the eco-friendly conversion of waste-into-bioenergy strategy.