Flowers are the most vulnerable plant organ to infection by the necrotrophic fungus, Botrytis cinerea. Here we show that pre-treatment of chrysanthemum flowers with phenylalanine (Phe) significantly reduces their susceptibility to B. cinerea. To comprehend how Phe-treatment induces resistance, we monitored the dynamics of metabolites (GC/LC-MS) and transcriptomes (RNAseq) in flowers post Phe-treatment and B. cinerea infection. Phe treatment resulted in accumulation of 3-phenyllactate and benzaldehyde, and in particular induced genes related to Ca²⁺ signaling and receptor kinases, implicating a defense response perception. Interestingly, the foremost response of Phe-treatment was in flowers exposed to B. cinerea infection, stabilizing the global fluctuations in the levels of metabolites and transcripts while reducing susceptibility to the fungus. We suggest that Phe-induced resistance is associated to cells priming, enabling rapid and targeted reprogramming of cellular defense responses to resist disease development. Phe pre-treatment maintained the levels of anti-fungal volatiles i.e. phenylacetaldehyde and eugenol, and strongly accumulated the levels of coniferin, a plausible monolignol precursor in cell wall lignification. In addition, Phe pre-treatment lessened the ROS generation, prevented the ethylene emission, and caused changes in expression of a minor number of genes with transcriptional reprogramming related to cell wall biogenesis, RLKs (THESEUS 1), Ca²⁺ and hormonal signaling processes. Our findings point to Phe pre-treatment as a potential orchestrator of a broad-spectrum defense response which may not only provide an ecological friendly control but also offers a promising way of priming plants to induce defense responses against B. cinerea.