The chemical immobilization of cobalt(II) ions in a silica aerogel matrix enabled the synthesis of the first representative example of aerogel-based single-ion magnets. For the synthesis of the lyogels, methyl-trimethoxysilane and N-3-(trimethoxysilyl)propyl ethylenediamine were co-hydrolyzed, then the ethylenediamine groups that were immobilized on the silica matrix enabled the subsequent binding of cobalt(II) ions. Lyogels with various amounts of ethylenediamine moieties (0.1–15 mol %) were soaked in isopropanol solutions of cobalt(II) nitrate and further supercritically dried in carbon dioxide to obtain aerogels with a specific surface area of 210–596 m2 ·g−1, an apparent density of 0.403–0.740 cm3·g−1 and a porosity of 60–78%. The actual cobalt content in the aerogels was 0.01–1.50 mmol per 1 g of SiO2, which could easily be tuned by the concentration of ethylenediamine moieties in the silica matrix. The introduction of cobalt(II) ions into the ethylenediamine-modified silica aerogel promoted the stability of the diamine moieties at the supercritical drying stage. The molecular prototype of the immobilized cobalt(II) complex, bearing one ethylenediamine ligand [Co(en)(MeCN)(NO3)2], was synthesized and structurally characterized. Using magnetometry in the DC mode, it was shown that cobalt(II)-modified silica aerogels exhibited slow magnetic relaxation in a nonzero field. A decrease in cobalt(II) concentration in aerogels from 1.5 mmol to 0.14 mmol per 1 g of SiO2 resulted in a weakening of inter-ion interactions; the magnetization reversal energy barrier likewise increased from 4 to 18 K.