Clonostachys rosea is an established biocontrol agent. Selected strains have either mycoparasitic activity against known pathogens (Fusarium species) and plant growth promoting activity on various crops. Here we report outcomes from a comparative omics analysis leveraging a temporal variation in the mycoparasitic activities of C. rosea strains ACM941 and 88-710, toward understanding the molecular mechanisms underpinning mycoparasitism.