Verticillium dahliae, a soil-borne fungal pathogen, causes wilt symptoms in dicots but not in monocots. The precise sequence when V. dahliae infects monocots and the underlying mechanisms by which these plants fend off V. dahliae remain unclear. In this study, we confirmed that V. dahliae can cause typical Verticillium wilt symptoms on dicots but not monocots. Scanning Electron Microscope (SEM) and Transmission electron microscope (TEM) studies indicate that V. dahliae conidia germinate, expand and penetrate into both dicot cotton and monocot maize roots initially but fail to survive in maize roots at later stages of infection. A large number of conidia and mycelia collapse in the maize root. The secretome of cotton isolate Vd991, induced in cotton and maize root about two days post-inoculation, indicate that the V. dahliae secretome likely contributes to the differential infection of the two hosts. CAZymes, oxidoreductases, and peptidases were differentially expressed in V. dahliae during infection of cotton versus maize, and a few of these have been identified as virulence factors during infecting cotton. The V. dahliae secretome likely contributes to the differences in the early infections between cotton and maize, and its inability to survive in maize root during later stages of infection.