Fusarium verticillioides, one of the most common pathogens in maize, is responsible for yield losses and reduced kernel quality due to contamination by fumonisins (FBs). Two F. verticillioides isolates that differed in their ability to produce FBs were treated with a selection of eight natural phenolic compounds with the aim of identifying those that were able to decrease toxin production at concentrations that had a limited effect on fungal growth. Among the tested compounds, ellagic acid and isoeugenol, which turned out to be the most effective molecules against fungal growth, were assayed at lower concentrations, while the first retained its ability to inhibit toxin production in vitro, the latter improved both the fungal growth and FB accumulation. The effect of the most effective phenolic compounds on FB accumulation was also tested on maize kernels to highlight the importance of appropriate dosages in order to avoid conditions that are able to promote mycotoxin biosynthesis. An expression analysis of genes involved in FB production allowed more detailed insights into the mechanisms underlying the inhibition of FBs by phenolic compounds. The expression of the fum gene was generally down-regulated by the treatments; however, some treatments in the low-producing F. verticillioides strain up-regulated fum gene expression without improving FB production. This study showed that although different phenolic compounds are effective for FB reduction, they can modulate biosynthesis at the transcription level in opposite manners depending on strain. In conclusion, on the basis of in vitro and in vivo screening, two out of the eight tested phenols (ellagic acid and carvacrol) appear to be promising alternative molecules for the control of FB occurrence in maize.