Solanum lycopersicum L. is affected among other pests and diseases, by the actinomycete Clavibacter michiganensis ssp. michiganensis (Cmm), causing important economic losses worldwide. The antimicrobial activity of mesoporous silica nanoparticles (MSN5.4), loaded with the recombinant antimicrobial peptides (AMP) human β-defensin-2 (hβD2) and assayed to inhibit Cmm. Half-maximum inhibitory concentration (IC50) of 3.64 μg/mL was quantified, while engineered TRX-hβD2-M and hβD2-M mutants, displayed an improvement inhibitory activity of IC50 of 3.64 and 1.56 μg/mL, respectively. MSNs had average particle sizes of 140 nm (SEM) and a tunable pore diameter of 4.8 up to 5.4 nm (BJH). AMPs were adsorbed more than 99% into MSN and a first release after 24 h was observed. The MSN loaded with the AMPs inhibited the growth of Cmm in solid and liquid media. It was also determined that MSNs protect AMPs from enzymatic degradation when the MSN/AMPs complexes were exposed to a pepsin treatment. An improved AMP performance was registered when it was adsorbed in the mesoporous matrix. The present study could expand the applications of MSNs loaded with AMPs as a biological control and provide new tools for the management of phytopathogenic microorganisms.