Recent advances in computer, communication and sensor/actuator technologies hint at an emerging paradigm of computing, popularly referred to as “digital ecosystems”. A Digital Ecosystem is a distributed, open socio-technical system composed of actors and services, with properties of self-organization, scalability and sustainability, inspired by natural ecosystems. A dramatic change of nature has recently affected digital ecosystems which should now be envisioned as multiscale highly heterogeneous systems at the convergence of the Internet of Things (IoT), mobile/ubiquitous computing and cloud/service-oriented computing. That is, future digital ecosystems will have to consider interaction processes that mobilize entities (typically, services) of totally different nature, origin and operational characteristics, from an embedded “thing” to a public cloud. In this talk, we will specifically focus on user-centric, ubiquitous and multi-scale digital ecosystems where users and services alike have (ubiquitous) access to a huge mass of information, produced by the local environment (sensor networks, ad-hoc networks, local servers) or remotely (Web services, distant servers, VPN-accessible private clouds, public clouds). Such digital ecosystems raise complex issues e.g., data indexing and access, data delivery, entities cooperation, scalability. However, the most sensitive issue may certainly be the enforcement of security properties and the preservation of privacy. In that perspective, the objective of this keynote is to draw an overview of security and privacy challenges in multi-scale digital ecosystems; to identify candidate methodologies to address these issues; and finally, to point out the main lines of a research agenda.