Rational design of silica ionogels requires an understanding of the impact of the synthesis route used on their properties and on their nanoscale architecture, which includes confinement effects. Here, the influence of the preparation method on the properties of silica-based ionogels loaded with 1-methyl-3-octylimidazolium bis(trifluoromethylsulfonyl)imide (OMIM TFSI) is discussed. The ionogels were prepared using three different approaches: (1) gelation of silica in OMIM TFSI ionic liquid (IL), (2) impregnation with OMIM TFSI of a silica wet-gel and (3) impregnation of a silica aerogel. The study revealed the pivotal impact of the ionogel preparation method on the reproducibility of the synthesis. Specifically, direct gelation of silica in the IL yielded ionogel monoliths with exceptional reproducibility. In contrast, impregnation approaches, which included additional stages, failed to produce monoliths in some (wet-gel impregnation) or all cases (aerogel impregnation). Generally, the ionogels prepared by the gelation and the wet-gel impregnation approaches presented very similar properties. Both ionogels were thermally stable (up to 200 °C), strong (compressive strength 0.7–1.2 MPa) and elastic (strain at break ε ∼ 10 %); they possessed relatively high ionic conductivity (1.9−3.4 μSm∙cm−1) and were reasonably stable upon contact with an aqueous medium. However, the ionogels prepared using different methods showed notable differences in their structure, in terms of the content and state of water and in terms of ion dynamics, and they demonstrated different IL confinement effects. The findings underscore that, for ionogels, the synthesis route taken affects both their structure and properties.