Vegetative Incompatibility (VI) can occur when filamentous fungi fuse during the asexual (mitotic) growth phase. In Cryphonectria parasitica, VI is modulated by six vic loci; hyphal fusion between strains that differ at one or more vic loci results in cell death. VI is considered an immune-like response that restricts heterokaryon formation and transmission of deleterious cytoplasmic elements through unknown mechanisms. A transcriptomic analysis of vic3-associated incompatibility identified a set of differentially expressed genes within biosynthetic gene clusters (BGCs). Using UPLC-HRMS, we detected significant shifts in secondary metabolite production during vic3 incompatibility. Among these metabolites, HPLC purification and NMR structure elucidation revealed that a new variant of calbistrin is linked to VI-upregulated BGCs, as is a farnesyl-S-oxide analog resembling mating pheromones. Similarly, detection of putative lysophosphatidylcholines and other modified lipids implicates membrane alteration during VI. Together, these findings suggest VI involves synthesis of novel secondary metabolites and complex membrane-associated signaling.