A global increase in the demand for olive oil has led to a current increase in the levels of by-products released from its production. The limited presence of these by-products over a short time period of the year and their large volumes, especially in Mediterranean countries, causes a challenge in terms of treating such substrates. Their eco-toxicological potential lies in their phytotoxicity and high organic charge, due in particular to the presence of polyphenols. Land disposal of such substrates is strictly limited or directly not permitted by law. Furthermore, the different composition of the substrates coming from the different systems of olive oil extraction makes it difficult to treat such substrates in an eco-friendly and definitive way. This review examines, in particular, the biotechnologically driven treatment of these by-products; especially in the production of biopolymers from the by-products released in the olive oil extraction process. These biopolymers could be either exopolysaccharides or polyhydroxyalkanoates. Moreover, such biopolymers can be produced by both the system of two-phase and three-phase olive oil production. In order to give a potential valorisation to these kinds of wastes in a biotechnological way, one of the most promising applications is in the production of bioplastics. This environment-friendly bioprocess, based on fermentation technology, could be the most suitable approach for competitive optimisation and produce an alternative to the thermoplastic polymers derived from crude oil.