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Purpose The biomedical applications of silver nanoparticles (AgNPs) are heavily investigated due to their cytotoxic and antimicrobial properties. However, the scientific literature is lacking in data on the aggregation behavior of nanoparticles, especially regarding its impact on biological activity. Therefore, to assess the potential of AgNPs in therapeutic applications, two different AgNP samples were compared under biorelevant conditions. Methods Citrate-capped nanosilver was produced by classical chemical reduction and stabilization with sodium citrate (AgNP@C), while green tea extract was used to produce silver nanoparticles in a green synthesis approach (AgNP@GTs). Particle size, morphology, and crystallinity were characterized using transmission electron microscopy. To observe the effects of the most important biorelevant conditions on AgNP colloidal stability, aggregation grade measurements were carried out using UV-Vis spectroscopy and dynamic light scatterig, while MTT assay and a microdilution method were performed to evaluate the effects of aggregation on cytotoxicity and antimicrobial activity in a time-dependent manner. Results The aggregation behavior of AgNPs is mostly affected by pH and electrolyte concentration, while the presence of biomolecules can improve particle stability due to the biomolecular corona effect. We demonstrated that high aggregation grade in both AgNP samples attenuated their toxic effect toward living cells. However, AgNP@GT proved less prone to aggregation thus retained a degree of its toxicity. Conclusion To our knowledge, this is the first systematic examination regarding AgNP aggregation behavior with simultaneous measurements of its effect on biological activity. We showed that nanoparticle behavior in complex systems can be estimated by simple compounds like sodium chloride and glutamine. Electrostatic stabilization might not be suitable for biomedical AgNP applications, while green synthesis approaches could offer new frontiers to preserve nanoparticle toxicity by enhancing colloidal stability. The importance of properly selected synthesis methods must be emphasized as they profoundly influence colloidal stability, and therefore biological activity.