We investigated the ageing of amine-terminated self-assembled monolayers (amine-SAMs) on different silica substrates due to exposure to different ambient gases, pressures, and/or temperatures using time-of-flight secondary ion mass spectrometry (ToF-SIMS) with principal component analysis and complementary methods of surface analysis as X-ray photoelectron spectroscopy (XPS) and near edge X-ray absorption fine structure (NEXAFS). The goal of this study is to examine the durability of primary amine groups of amine-SAMs stored in a user laboratory prior to being used as supports for biomolecule immobilization and other applications. We prepared amine-SAMs on the native oxides of silicon wafers and glass slides using 3-aminopropyl triethoxysilane, by using optimized conditions such as anhydrous organic solvent and reaction time scale of hours to avoid multilayer growth. Selected commercial amine-SAM slides have been investigated, too. When the amine-SAMs are exposed to air, oxygen incorporation occurs, followed by formation of amide groups. The formation of oxygen species due to ageing was proved by ToF-SIMS, XPS, and NEXAFS findings such as CNO(-) secondary ion emission at m/z 42, observation of the N 1s HNC=O component peak at 400.2-400.3 eV in XPS, and, last but not least, by formation of a π*(HNC=O) resonance at 401 eV in the N K-edge X-ray absorption spectrum. It is concluded that the used multi-method approach comprising complementary ToF-SIMS, XPS, and NEXAFS analyses is well suited for a thorough study of chemical aspects of ageing phenomena of amine-SAM surfaces.