Witches' broom is a major disease of cacao, limiting cocoa production in South America. The basidiomycete Moniliophthora perniciosa, the disease causative agent, presents hemibiotrophic lifestyle with an extensive biotrophic period, promoting typical symptoms of hypertrophic growth of stems and proliferation of axillary shoots. The tomato (Solanum lycopersicum) cv. 'Micro-Tom' (MT) is a suitable genetic model to study pathogenic interaction of S-biotype M. perniciosa, exhibiting typical symptoms of the infection. Considering the lack of knowledge regarding biochemical and physiological mechanisms of M. perniciosa pathogenesis, this study aimed to investigate physiological and metabolic changes during MT infection of M. perniciosa. Inoculation of M. perniciosa caused stem thickening, leaf chlorosis and reduction in root growth and fruits in MT. We also observed a decline in photosynthetic rate (A), stomatal closure, increase in intracellular CO2, decrease in leaf transpiration and an increase on stem Proline, polyamines, and ascorbate oxidation exhibits an oxidative stress environment at the site of MT infection, whereas the accumulation of raffinose and GABA suggests ROS neutralization, mitigating its harmful effects. At 30 DAI, carbon reallocation and sugar signaling pathways were shifted. Sucrose exogenous application in MT infected plants by M. perniciosa reduced symptoms of stem swelling, but did not reduce root growth or number of fruits. Inoculation of single-flower truss sft mutant and its opposite 35S::SFT with M. pernciosa demonstrated that pathogen infection did not affect transition from vegetative to reproductive meristem, but decreased the development of flowers. Finally, inoculation of lutescent and green flesh senescence mutants neither altered symptoms of infection, nor enabled the observation of necrosis of infected tissue in MT background, as observed in cacao infected by M. perniciosa. A model for biochemical and physiological changes during MT infection by M. perniciosa was proposed.