This dataset comprises site-specific glycopeptide analysis of complement component C3 from plasma samples of 816 adults from the Korčula cohort (Croatia). C3 glycopeptides were enriched using Concanavalin A lectin affinity chromatography and analyzed by nano-LC-MS/MS. The study characterizes the N-glycan repertoire at both occupied glycosylation sites (N63 and N917), which carry exclusively high-mannose structures including unusual monoglucosylated glycoforms (Glc1Man9GlcNAc2, Glc1Man8GlcNAc2). Glycopeptide quantification was performed to assess associations with demographic and biochemical traits, and to conduct genome-wide association analysis identifying genetic determinants of C3 glycosylation. This represents the first large-scale population-level analysis of site-specific C3 N-glycosylation.