Fungi occupy an incredibly diverse range of biological niches, including symbiotic, commensal, and pathogenic relationships with other organisms. The cell wall of the fungus is the first point of contact and the major mediator of these interactions. Research strategies to control fungal disease and boost beneficial relationships must account for cell wall biosynthesis and remodelling. We hypothesised that extracellular vesicles (EVs) and non-classical secretion pathways are essential for cell wall remodelling during the response to cell wall perturbation in fungi. In this study, extracellular vesicles of the model yeast Saccharomyces cerevisiae were analysed using LC-MS bottom-up proteomics to assess the impact of gene knockouts in key cell wall biosynthetic pathways. Independent gene deletions affecting the major cell wall carbohydrates 1,3-beta-glucan and chitin mimicked the effect of antifungal strategies and allowed assessment of cell wall remodelling and the response to these interventions. Disruption of chitin biosynthesis resulted in increased EV load for proteins related to cellular localisation and transport and decreased abundances for primary metabolic pathways. Disruption of 1,3-beta-glucan biosynthesis saw an increased EV load of cytosol-annotated proteins and a loss of EV proteins required for bud formation and cell division. These findings suggest disruption of cell wall biosynthesis in the fungi exerts unique influences on EV proteins dependent on the structural carbohydrate.