We developed a facile and greener approach for the preparation of silica-aerogel-based ionogels using choline dihydrogen phosphate ionic liquid by the sol–gel approach. A series of silica-based aerogels as ionogels were prepared by varying the ionic liquid concentrations: 0.1, 0.5, 1, 3, 5, and 10 wt %. The as-prepared ionogels were characterized using several analytical techniques, namely, attenuated total reflectance (ATR)/FT-IR, TGA, XRD, and particle size analyses. The role of ionic liquid in the viscoelastic properties of the sol–gel transition was monitored using time-dependent rheological measurements. The addition of ionic liquid to the sol–gel system favored the formation of a more interconnected silica network structure. The formation of a silica network structure during sol–gel hydrolysis and condensation was confirmed from 29Si solid-state CP/MAS NMR spectra. The effect of the ionic liquid on the morphological properties was investigated using SEM and TEM studies. The cell viabilities of the prepared gel samples were clearly evident from the cytotoxicity assay studies using Swiss and HaCaT cells. The main advantages of using biocompatible ionic liquids for the preparation of these aerogels as ionogels are that they may be used for encapsulating biological molecules and retain their conformational stability for a longer duration.