Humans face the risk of exposure to silver nanoparticles (AgNPs) due to their extensive application in consumer products. AgNPs can interact with many substances in the human body due to their chemically unstable nature and high activity properties, which might result in unknown hazards and even some serious diseases for humans. As the basic constituent element of human bodies, amino acids (AAs) differ in concentration and variety in different cells and tissues. Thus, understanding the transformation of citrate-coated AgNPs in the presence of AAs is crucial for determining their fate and toxicity in the human body. Our study focused on the transformation of the morphology, dissolution behavior and reaction product of AgNPs in different AA-containing systems and then evaluated the effect of these transformations on the cytotoxicity of AgNPs. The obtained results indicated that the addition of glycine with the lowest Ag(+) binding energy had little effect on the transformations and toxicity of AgNPs. While in the presence of histidine with higher Ag(+) binding energy, the Ag(+) release and particle size of AgNPs obviously increased. These transformations resulted in a decrease in the cytotoxicity of AgNPs due to the formation of Ag-His complex and the growth of AgNPs. Furthermore, l-cysteine with the highest Ag(+) binding energy could easily interact with AgNPs, transforming them completely to form [Ag(Cys)n](+) and Ag2S precipitates, which induced the largest decrease in AgNP toxicity. In summary, our results may provide useful information to understand the fate, transformation, and toxicity of citrate-coated AgNPs in the human body.