Cell walls underpin the mechanics of cell growth, intercellular signalling, and defence against pathogenic organisms. β-(1,3)-glucans (also known as callose) are polysaccharides found in plants, fungi, and some bacterial species. In developing plant organs, callose accumulates around intercellular channels (plasmodesmata) controlling cell-to-cell communication. We developed monoclonal antibodies for the detection of β-(1,3)-glucans and using these identified distinct populations of callose differing in size and secondary structure. Callose sub-populations were in proximal but not overlapping cell wall microdomains implying distinct spatial and functional microenvironments. We also unveiled callose interaction with xyloglucan; another plant glycan regulating cell wall functions. This work challenges previous views demonstrating structural heterogeneity in plant callose and supporting interactions between glycans with roles in the regulation of cell wall properties and functions.