Beneficial fungi in the genus
Trichoderma
are among the most widespread biocontrol agents of plant pathogens. Their role in triggering plant defenses against pathogens has been intensely investigated, while, in contrast, very limited information is available on induced barriers active against insects. The growing experimental evidence on this latter topic looks promising, and paves the way toward the development of
Trichoderma
strains and/or consortia active against multiple targets. However, the predictability and reproducibility of the effects that these beneficial fungi is still somewhat limited by the lack of an in-depth understanding of the molecular mechanisms underlying the specificity of their interaction with different crop varieties, and on how the environmental factors modulate this interaction. To fill this research gap, here we studied the transcriptome changes in tomato plants (cultivar “Dwarf San Marzano”) induced by
Trichoderma harzianum
(strain T22) colonization and subsequent infestation by the aphid
Macrosiphum euphorbiae
. A wide transcriptome reprogramming, related to metabolic processes, regulation of gene expression and defense responses, was induced both by separate experimental treatments, which showed a synergistic interaction when concurrently applied. The most evident expression changes of defense genes were associated with the multitrophic interaction
Trichoderma
-tomato-aphid. Early and late genes involved in direct defense against insects were induced (i.e.,
peroxidase, GST, kinases and polyphenol oxidase, miraculin, chitinase
), along with indirect defense genes, such as
sesquiterpene synthase
and
geranylgeranyl phosphate synthase
. Targeted and untargeted semi-polar metabolome analysis revealed a wide metabolome alteration showing an increased accumulation of isoprenoids in
Trichoderma
treated plants. The wide array of transcriptomic and metabolomics changes nicely fit with the higher mortality of aphids when feeding on
Trichoderma
treated plants, herein reported, and with the previously observed attractiveness of these latter toward the aphid parasitoid
Aphidius ervi
. Moreover,
Trichoderma
treated plants showed the over-expression of transcripts coding for several families of defense-related transcription factors (bZIP, MYB, NAC, AP2-ERF, WRKY), suggesting that the fungus contributes to the priming of plant responses against pest insects. Collectively, our data indicate that
Trichoderma
treatment of tomato plants induces transcriptomic and metabolomic changes, which underpin both direct and indirect defense responses.