Abstract Environmental DNA-based research is undergoing rapid developments, but its democratization in basic and applied research remains hampered by the biases introduced by molecular approaches, the difficulties in estimating absolute organisms’ abundances, and a lack of general consensus in molecular protocols. Chapter 19 “The future of eDNA metabarcoding” provides an overview of these current challenges and discusses how shotgun sequencing, capture-based methods, inclusion of internal standards, and development of new data repositories could alleviate these limits and facilitate cross-experiments comparisons. This chapter finally turns to open questions on the potentiality of new sequencing methods and proposes directions to improve biodiversity estimates and ecological inferences and predictions from eDNA data, and ultimately stimulate further developments and integration of eDNA metabarcoding into academic and operational ecological research and monitoring.