Silica particles synthesized by precipitation method were in situ capped with Ethylenediaminetetraacetic acid (EDTA) and Hexamethylenetetramine (HMTA) compounds aiming to increase their biocompatibility. XRD, FTIR, TG/DSC, DLS and SEM analyses were performed to determine the crystalline structure, attached functional groups, thermal behaviour, size and morphology of silica particles. XRD analysis showed the amorphous structure of synthesized particles. FTIR results confirmed the formation of SiO2 particles and pointed about the functional groups (−CN, −CO,−OH etc.) attached on surface. Thermal analysis results showed that weight loss was due to removal of water and gradual degradation of EDTA molecules with rise of temperature, i.e. above 220 °C. The dynamic laser scattering measurements (zeta potential) depicted the strongest electrophoretic stability (− 30 mV) of EDTA-capped silica than virgin (− 13 mV) and particles capped with HMTA(− 24 mV). The SEM results revealed that virgin and silica particles capped with EDTA ligand exhibited spherical morphology with an average particle size of 210 nm and 280 nm, respectively. Whereas, HMTA-capped silica partilces showed hexagonal morphology with an average particle size of 240 nm. The in vitro cytotoxicity analysis was also carried out using human HepG2w, ATCC® HB-8065™ cell culture of 100 µg/ml concentration in Dulbecco’s Modified Eagle Medium (DMEM) solution maintained at 37 °C in the presence of CO2 environment. The results revealed that silica particles capped with EDTA (0.07 g) have shown remarkable biocompatibility (~ 96%) than virgin silica (~ 69%) due to bearing better hydrophobic characteristics. However, HMTA decomposed during synthesis which induced toxicity and agglomeration among silica particles. As a result, poor biocompatibility (~ 65%) was observed.