The present work introduces both synthesis of silica nanoparticles doped with Co^II ions by means of differently modified microemulsion water-in-oil (w/o) and Stöber techniques and characterization of the hybrid nanoparticles (Co^II@SiO₂) by TEM, DLS, XRD, ICP-EOS, SAXS, UV-Vis, and UV-Vis/DR spectroscopy and electrochemical methods. The results reveal the lack of nanocrystalline dopants inside the hybrid nanoparticles, as well as no ligands, when Co^II ions are added to the synthetic mixtures as Co^II(bpy)₃ complexes, thus pointing to coordination of Co^II ions with Si-O^- groups as main driving force of the doping. The UV-Vis/DR spectra of Co^II@SiO₂ in the range of d-d transitions indicate that Stöber synthesis in greater extent than the w/o one stabilizes tetrahedral Co^II ions versus the octahedral ions. Both cobalt content and homogeneity of the Co^II distribution within Co^II@SiO₂ are greatly influenced by the synthetic technique. The electrochemical behavior of Co^II@SiO₂ is manifested by one oxidation and two reduction steps, which provide the basis for electrochemical response on glyphosate and HP(O)(OEt)₂ with the LOD = 0.1 μM and the linearity within 0.1–80 μM. The Stöber Co^II@SiO₂ are able to discriminate glyphosate from HP(O)(OEt)₂, while the w/o nanoparticles are more efficient but nonselective sensors on the toxicants.