Beneficial rhizobacterium Pseudomonas fluorescens N 21.4 and its metabolic elicitors inoculated to cultivars of blackberry (Rubus spp. Var. Loch Ness) reinforced the plants’ immune system and improved their fitness by increasing photosynthesis, decreasing oxidative stress, and activating pathogenesis-related proteins. They also triggered the leaves’ flavonoid metabolism, enhancing the accumulation of beneficial phenolic compounds such as kaempferols and quercetin derivatives. The elicitation of leaf secondary metabolism allows one to take advantage of the blackberry leaves (a current crop waste), following the premises of the circular economy, to isolate and obtain high added value compounds. The results of this work suggest the use of N 21.4 and/or its metabolic elicitors as plant inoculants as an effective and economically and environmentally friendly agronomic alternative practice in the exploitation of blackberry crops to obtain plants with a better immune system and to revalorize the leaf pruning as a potential source of polyphenols.