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Simple Summary Olive oil is the most common vegetable oil used for human nutrition, and its production represents a major economic sector in Mediterranean countries. The milling industry generates large amounts of liquid and solid residues, whose disposal is complicated and costly due to their polluting properties. However, olive mill waste (OMW) may also be seen as a source of valuable biomolecules including plant nutrients, anthocyanins, flavonoids, polysaccharides, and phenolic compounds. This review describes recent advances and multidisciplinary approaches in the identification and isolation of valuable natural OMW-derived bioactive molecules. Such natural compounds may be potentially used in numerous sustainable applications in agriculture such as fertilizers, biostimulants, and biopesticides in alternative to synthetic substances that have a negative impact on the environment and are harmful to human health. Abstract Olive oil production generates high amounts of liquid and solid wastes. For a long time, such complex matrices were considered only as an environmental issue, due to their polluting properties. On the other hand, olive mill wastes (OMWs) exert a positive effect on plant growth when applied to soil due to the high content of organic matter and mineral nutrients. Moreover, OMWs also exhibit antimicrobial activity and protective properties against plant pathogens possibly due to the presence of bioactive molecules including phenols and polysaccharides. This review covers the recent advances made in the identification, isolation, and characterization of OMW-derived bioactive molecules able to influence important plant processes such as plant growth and defend against pathogens. Such studies are relevant from different points of view. First, basic research in plant biology may benefit from the isolation and characterization of new biomolecules to be potentially applied in crop growth and protection against diseases. Moreover, the valorization of waste materials is necessary for the development of a circular economy, which is foreseen to drive the future development of a more sustainable agriculture.