Biogas plants receive inputs of different sources of carbon, nutrients, metals and other pollutants from large areas that result in a digestate that is a very complex and concentrated matrix. How to redistribute all these components without causing imbalances in the receiving environments is one of the main questions that arises regarding the reuse of digestate. The main end destinations of digestate within the EU are agriculture, landfill and incineration, in addition to open-mine land reclamation. There are European and country specific end destinations of digestate that have been recently reviewed and made publicly available in an EU commission report. In terms of agricultural application, digestate is seen as a valuable source of carbon and nutrients, but its application is conditioned by disposal limits for nitrogen, phosphorous and metals. Here, we discuss the need for redesign of the process of digestate manipulation in order to increase its value as fertiliser, through addition of compounds, different solid/liquid phases separation or additional treatments. Potential recovery techniques are also discussed. Phytoremediation, the use of plants to uptake metals from different substrates, can be used not only to remove trace metals from the digestate but also for the recovery of metals from plant biomass or their reintroduction into the biodigester. In addition, a combination of landfill with phytoremediation can be a good alternative for the recovery of degraded soils, or for the reclamation of polluted soil for landscape recovery. Another option can be the use of digestate to produce biochar to be applied in agriculture, a technique that increases carbon content in soils while decreasing trace metal bioavailability. Finally, we discuss the new opportunities that are arising for the use of digestate, including microalgae biomass production and bioenergy.