Plants are continuously exposed to the attack of invasive microorganisms, such as fungi or bacteria, and also viruses. To fight these attackers, plants develop different metabolic and genetic responses whose final outcome is the production of either toxic compounds that kill the pathogen or deter its growth, and/or semiotic molecules that alert other individuals from the same plant species. These molecules are derived from the secondary metabolism and their production is induced upon detection of a pathogen-associated molecular pattern (PAMP). These PAMPs are different molecules that are perceived by the host cell triggering defense responses. PAMP-elicited compounds are highly diverse and specific of every plant species and can be divided into preformed metabolites or phytoanticipins that are converted into toxic molecules upon pathogen perception, and toxic metabolites or phytoalexins that are produced only upon pathogen attack. Moreover, plant volatile emissions are also modified in response to pathogen attack to alert neighboring individuals or to make plants less attractive to pathogen vector arthropods. Plant metabolite profiling techniques have allowed the identification of novel antimicrobial molecules that are induced upon elicitation. However, more studies are required to assess the specific function of metabolites or metabolite blends on plant-microbe interactions.