Nanoscale ionophore-based ion-selective optodes (nano-ISOs) are effective sensing tools for in situ and real time measurements of ion concentrations in biological and environmental samples. While searching for novel sensing materials, nano-ISOs free of plasticizers are particularly important for biological and environmental applications. This work described plasticizer-free nano-ISOs based on Si-containing particles including PEGylated organosilica nanoparticles, PDMS nanospheres, and SiO microspheres, with diameters around 50 nm, 100 nm, and 5 μm, respectively. The platform enabled the use of highly selective ionophores, where the nanomatrices played important roles in tuning the ion-carrier complex formation constants and led to better selectivity for the PEGylated organosilica nano-ISOs than those based on PDMS. With use of the versatile silica chemistry, pH and ion dual sensing was achieved on SiO microspheres. In addition, increasing the cross-linking degree of the PDMS nano-ISOs extended the linear response range, and cellular uptake experiments showed that the nano-ISOs could readily enter HeLa cells with very low cytotoxicity.