Engineered nanomaterials, particularly silver nanoparticles (AgNPs), have emerged as promising tools in oncology due to their ability to enhance tumor targeting and minimize off-target effects. This study investigates the cytotoxic effects of two different types of AgNPs-citrate-coated (AgNPs-cit) and EGOH-coated (AgNPs-EGOH)-on colorectal cancer (CRC) cell lines and healthy colonocytes, aiming to assess their potential as selective therapeutic agents. AgNPs-cit and AgNPs-EGOH were synthesized and characterized for size and surface properties. LoVo (microsatellite instability-high) and HT-29 (microsatellite stable) CRC cell lines, along with primary colonocyte cultures from healthy mucosal tissues, were exposed to these nanoparticles. Cytotoxicity was assessed through MTT assays, while morphological changes were observed using fluorescence microscopy. Internalization of the nanoparticles was evaluated by confocal microscopy. AgNPs-cit exhibited significant cytotoxicity in LoVo cells, reducing viability and inducing morphological changes indicative of programmed cell death, especially after 48 h of exposure. In contrast, AgNPs-EGOH showed minimal effects on LoVo cells and no significant toxicity on HT-29 cells or primary colonocytes. Confocal microscopy confirmed nanoparticle internalization, with surface functionalization influencing the distribution patterns within cells. This study demonstrates that surface functionalization significantly influences the cytotoxicity of AgNPs, with citrate-coated nanoparticles showing selective effects on microsatellite instability-high CRC cells. These findings underscore the potential of surface-modified nanoparticles for targeted cancer therapy and highlight the importance of tailoring nanoparticle design to optimize therapeutic efficacy while minimizing off-target effects.