Significance Statement IgA nephropathy (IgAN) is the most common primary glomerular disease worldwide, with galactose-deficient IgA (gd-IgA) considered to play a key role in its pathogenesis. Although this association is widely reported, it is unclear how IgA glycosylation changes with the disease. A novel mass spectrometry–based approach provided a more complete picture of IgA glycosylation changes in IgAN and of the relationship between IgA glycosylation and kidney function. Multiple structural features of both O- and N-linked glycans were associated with the presence and severity of IgAN and kidney function. Our high-resolution data suggest that IgA O- and N-glycopeptides are promising targets for future studies on the pathophysiology of IgAN and as potential noninvasive biomarkers for disease prediction. Background IgA nephropathy (IgAN) is the most common primary glomerular disease worldwide and is a leading cause of renal failure. The disease mechanisms are not completely understood, but a higher abundance of galactose-deficient IgA is recognized to play a crucial role in IgAN pathogenesis. Although both types of human IgA (IgA1 and IgA2) have several N-glycans as post-translational modification, only IgA1 features extensive hinge-region O-glycosylation. IgA1 galactose deficiency on the O-glycans is commonly detected by a lectin-based method. To date, limited detail is known about IgA O- and N-glycosylation in IgAN. Methods To gain insights into the complex O- and N-glycosylation of serum IgA1 and IgA2 in IgAN, we used liquid chromatography-mass spectrometry (LC-MS) for the analysis of tryptic glycopeptides of serum IgA from 83 patients with IgAN and 244 age- and sex-matched healthy controls. Results Multiple structural features of N-glycosylation of IgA1 and IgA2 were associated with IgAN and glomerular function in our cross-sectional study. These features included differences in galactosylation, sialylation, bisection, fucosylation, and N-glycan complexity. Moreover, IgA1 O-glycan sialylation was associated with both the disease and glomerular function. Finally, glycopeptides were a better predictor of IgAN and glomerular function than galactose-deficient IgA1 levels measured by lectin-based ELISA. Conclusions Our high-resolution data suggest that IgA O- and N-glycopeptides are promising targets for future investigations on the pathophysiology of IgAN and as potential noninvasive biomarkers for disease prediction and deteriorating kidney function.