Fusarium graminearum is a major plant pathogen that causes devastating diseases of cereals and produces type B trichothecene mycotoxins (TCTB) in infected grains. A comprehensive understanding of the molecular and biochemical mechanisms underlying the regulation of TCTB biosynthesis is required for improving strategies to control the TCTB contamination of crops and ensuring that these strategies do not favor the production of other toxic metabolites by F. graminearum Elucidation of the association of TCTB biosynthesis with other central and specialized processes was the focus of this study. Combined 1H-NMR and LC-QTOF-MS analyses were used to compare the exo- and endo- metabolomes of F. graminearum grown in toxin-inducing and repressing caffeic acid-conditions. Ninety-five metabolites were putatively or unambiguously identified including 26 primary and 69 specialized metabolites. Our data demonstrated that the inhibition of TCTB production induced by caffeic acid exposure was associated with significant changes in secondary and primary metabolism of F. graminearum although the fungal growth was not affected. The main metabolic changes were an increase in the accumulation of several polyketides including toxic ones, alterations in the tricarboxylic organic acid cycle and modifications in the metabolism of several amino-acids and sugars. While these findings provide insights into the mechanisms that govern the inhibition of TCTB production by caffeic acid, they also demonstrate the interdependence between the biosynthetic pathway of TCTB and several primary and specialized metabolic pathways. These results provide further evidence of the multifaceted role of TCTB in the life cycle of F. graminearumIMPORTANCEFusarium graminearum is a major plant pathogen that causes devastating diseases of cereal crops and produces type B trichothecene (TCTB) mycotoxins in infected grains. The best way to restrict consumer exposure to TCTB is to limit their production before harvest, which requires increasing the knowledge on the mechanisms that regulate their biosynthesis. Using a metabolomics approach, we investigated the interconnection between the TCTB production and several fungal metabolic pathways. We demonstrated that alteration in the TCTB biosynthetic pathway can have a significant impact on other metabolic pathways including the biosynthesis of toxic polyketides and vice versa These findings open new avenues for identifying fungal targets for the design of molecules with anti-mycotoxin properties and therefore improving sustainable strategies to fight against F. graminearum-caused diseases. Our data further demonstrate that analyses should consider all fungal toxic metabolites rather than the targeted family of mycotoxins when assessing the efficacy of control strategies.