The stimulation of plant innate immunity by elicitors is an emerging technique in agriculture that contributes more and more to residue-free crop protection. Here, we used RNA-sequencing to study gene transcription in tomato leaves treated three times with the chitooligosaccharides–oligogalacturonides (COS-OGA) elicitor FytoSave ® that induces plants to fend off against biotrophic pathogens. Results showed a clear upregulation of sequences that code for chloroplast proteins of the electron transport chain, especially Photosystem I (PSI) and ferredoxin. Concomitantly, stomatal conductance decreased by half, reduced nicotinamide adenine dinucleotide phosphate [NAD(P)H] content and reactive oxygen species production doubled, but fresh and dry weights were unaffected. Chlorophyll, β-carotene, violaxanthin, and neoxanthin contents decreased consistently upon repeated elicitations. Fluorescence measurements indicated a transient decrease of the effective PSII quantum yield and a non-photochemical quenching increase but only after the first spraying. Taken together, this suggests that plant defense induction by COS-OGA induces a long-term acclimation mechanism and increases the role of the electron transport chain of the chloroplast to supply electrons needed to mount defenses targeted to the apoplast without compromising biomass accumulation.