Three experimental treatments consisting of inoculation with an arbuscular mycorrhizal fungus, application of a synthetic antimicrobial peptide or application of a resistance inducer, were evaluated in Madagascar periwinkle as control methods for rubus stunt and stolbur diseases caused by ‘ Candidatus Phytoplasma rubi’ and ‘ Candidatus Phytoplasma solani’, respectively. Two experiments were conducted under controlled environment conditions. In the first experiment, 4 months after graft‐inoculating the phytoplasmas, the root colonization achieved by Rhizophagus irregularis significantly reduced both disease symptoms and the frequency of detection of the pathogens by real‐time PCR . In the second experiment, the antimicrobial peptide BP 100 totally prevented disease symptoms, despite the molecular detection of the phytoplasmas in 75% and 50% of the plants inoculated with ‘ Ca . Phytoplasma rubi’ and ‘ Ca . Phytoplasma solani’, respectively, and was more effective than benzothiadiazole ( BTH ) at increasing resistance against the pathogenic infections. A potential combination of early mycorrhizal inoculation and BP 100 antimicrobial peptide application is envisaged as a future control strategy for phytoplasma diseases.