Cinnamic acid (CA) is an allelochemical that inhibits the growth of root promoting soil microorganisms. To prevent the growth of soil microbes, CA modulates several metabolic pathways in host plants and soil microbes. The aim of the current study was to investigate the effect of CA on maize root growth, exudation of secondary metabolites and its interaction with beneficial endophyte Pz11. The endophyte Pz11 was isolated from the roots of drought stressed Asphodelus tenuifolius (wild onion). The Pz11 strain was identified as Fusarium culmorum by homology of the internal transcribed spacer (ITS) region of 18 S rDNA sequence. The F. culmorum Pz11 produced phytostimulants and signaling compounds, such as indole-3-acetic acid (IAA), flavonoids and sugars. Moreover, the strain have effectively colonized the roots of maize and subsequently enhanced the growth of its host plants. On the contrary, application of CA has reduced root growth in maize seedlings as well as root colonization ability of F. culmorum Pz11. Also, maize seedlings exposed to CA exude low quantities of flavonoids and polyphenols. In conclusion, CA reduces the maize root growth and exudation of secondary metabolites, which may affects its ability to attract plant growth promoting endophytic fungi.