Manganese oxide–silica mixed oxide aerogels with different morphological and chemical properties were prepared using the sol–gel method and ensuing extraction of the solvent with supercritical CO2. Two types of manganese precursor, varying hydrolysis conditions of the silica and manganese precursors, influence of base addition for gelation, and calcination temperatures were investigated. Base addition had a strong effect on textural properties, producing high-surface-area, mesoporous aerogels, whereas these properties were only marginally affected by kind of manganese precursor used. The presence of different manganese oxide species was evidenced by X-ray diffraction, Raman and diffuse reflectance infrared Fourier transform spectroscopy, and temperature-programmed reduction. Mn4+, Mn3+, and Mn2+ oxide species were found after calcination at 600°C in air. Sol–gel processing with manganese(II) nitrate resulted in highly dispersed mixed oxides. Basic gelation of these sols strongly influenced the state of the manganese, leading to crystallites of hausmannite and to amorphous Mn5O8 in the calcined samples. Aerogels derived from the less reactive Mn(III) (acac)3 did not contain any manganese oxide crystallites when prepared under the same basic conditions. The catalytic performance of the aerogels in the selective oxidation of ammonia strongly depended on the state of the manganese. Samples containing crystalline Mn3O4 were more active than amorphous aerogels with dispersed manganese oxide species and afforded high selectivity to N2O. The presence of amorphous Mn5O8 further increased the activity and the selectivity to nitrous oxide, reaching 74% at 360°C. Nitrogen formation was found to be related to the amount of strongly Lewis-bound ammonia. The amorphous aerogels showing more Lewis-bound ammonia produced mainly nitrogen below 480°C, affording a selectivity of 78% at 360°C.