Fungal growth in fruits may cause spoilage and result in a reduction of their quality and quantity. The aim of the current study was to investigate the antifungal activity and the metabolism of thymol and carvacrol by Colletotrichum acutatum and Botryodiplodia theobromae. The results showed that both compounds provided relatively good control against these plant pathogenic fungi. Mycelial growth of C. acutatum and B. theobromae was inhibited at 50 µg/mL and above. At 150 µg/mL, thymol and carvacrol inhibited the radial growth of fungi completely and this effect remained for 240 h. Furthermore, thymol and carvacrol were metabolized by the plant pathogenic fungi in low proportion to several compounds, including thymoquinone, thymohydroquinone, thymyl- and carvacryl acetate, thymyl- and carvacryl methyl ether. The transformations affect the structural requirements of thymol and carvacrol related to their antimicrobial activity and mode of action. The relatively high antifungal activity of thymol and carvacrol against C. acutatum and B. theobromae and the low levels of microbial transformation indicate that both compounds could be an alternative to traditional chemical fungicides for control of pre- and postharvest phytopathogenic fungi on fruits or vegetables.