The overall goal of ERA Chair/EnvMetaGen project No 668981 is to expand the research and innovation potential of InBIO – Research network in Biodiversity and Evolutionary Biology, through the creation of an ERA Chair in Environmental Metagenomics. This field was selected as the focus of the ERA Chair, because Environmental DNA (eDNA) analysis is increasingly being used for biodiversity assessment, diet analysis, detection of rare or invasive species, population genetics and ecosystem functional analysis. In this context, the work plan of EnvMetaGen includes one work package dedicated to the Deployment of an eDNA Lab (WP4), which involves the training of InBIO researchers and technicians for implementing best practice protocols for the analysis of eDNA (Task 4.2). These protocols are essential for key application areas and to the development of research projects in association with business partners and other stakeholders, and thus to the strengthening of InBIO triple-helix initiatives (InBIO-Industry-Government; WP5). This report provides an overview of the current state of the art for collecting and preserving eDNA samples, with particular focus on vertebrate faecal samples, water samples and bulk invertebrate samples, which have been selected as key targets for the development of triple helix strategic initiatives (Task 5.3). The protocols already optimized and currently under development for the collection and preservation of eDNA samples are reported herein. Moreover, the future directions of sample collection and preservation at InBIO are discussed. This development was made possible through the recruitment of the ERA Chair team (WP2), secondments and Junior Researcher exchanges through the collaboration with international networks (WP3), an enhancement of computational infrastructure at InBIO (WP4) and participation of team members in workshops and conferences (WP6). Together, Deliverables D4.2-D4.5 (this document; Ferreira et al. 2018; Galhardo et al. 2018; Paupério et al. 2018) form a detailed account of the successful deployment of a fully functional eDNA lab under the EnvMetaGen project, and provide a valuable resource for eDNA practitioners in all spheres of the triple-helix model.