Abstract Background Recently, a novel concept ‘bio-effectors’ rose on to describe a group of products that are able to improve plant performance rather than fertilizers. Agro-food processing residues and by-products potentially represent important sources of bio-effectors but they are currently not properly taken in consideration. To fulfill this gap, in these study, three food processing by-products: (i) brewers' spent grain, (ii) fennel processing residues, and (iii) lemon processing residues were chosen as bio-effector candidates. Raw materials were chemically characterized, and green extraction methodology was optimized by using water, ethanol, and their mixture based on the extraction yields. Aqueous extracts were used for seed germination bioassays on Lepidium sativum seeds to evaluate their potential bioactivities. Thereafter, the extracts were chemically characterized and metabolites were detected by 1D and 2D NMR spectroscopy. Results Results are summarized as follows: (i) raw materials showed an interesting nutritional content; (ii) aqueous extraction resulted higher yield more than other used solvent; (iii) at high solvent extraction ratio, aqueous extracts were not phytotoxic but enhanced seed germination and root elongation; ( iv ) all aqueous extracts are differently rich in nutrients, amino-acids, sugars, and other low molecular weight molecule compounds. Conclusions This study confirmed that efficient and simple recovery of bioactive compounds other than nutrients from agro-food processing by-products appear to be the new frontier in their valorization. Graphical Abstract ᅟ