Site-specific conjugation is one of the promising research areas in antibody–drug conjugate (ADC) development, allowing for controlled conjugation and production of homogeneous ADCs, contrary to highly heterogeneous early-generation ADCs. We report here the characterization of a site-specific DAR2 ADC generated through glycan-based enzymatic remodeling and click chemistry (GlyCLICK™), using innovative native mass spectrometry (nMS) methods. The conjugation process was monitored with size exclusion chromatography coupled to nMS (SEC-nMS) for straightforward identification and quantification of all reaction species. Ion mobility-based collision-induced unfolding (CIU) approaches were used to assess the gas-phase behavior and the resistance to unfolding of the products along the synthesis.