While S3 has reached the status of a common policy tool at the EU level and beyond, recent experiences show that development and implementation are far from trivial. This working paper addresses this challenge by operationalising S3 implementation through a novel focus on the concept of Transformative Activities (TA). TA are defined as a collection of related innovation capacities and actions, extracted from existing structures and oriented toward a certain direction of change. The systematic identification and development of these activities is a complex exercise requiring new tools to support the entrepreneurial discovery and action development process. In response, we draft a workshop methodology including generic considerations on funding mechanisms, the necessary base of evidence and the relevant actors to be involved in the process. The process as such is structured in three phases: pre-determination of covered fields (Phase 0), identification and prioritisation of TA (Phase I) and development of action plans for the identified TA (Phase II). In order to focus the workshops and allow the practical organisation of the workshops, the fields to be covered need to be pre-determined in a preliminary phase. The first phase of the workshop then consists of assessing existing capacities and opportunities and evaluating the relatedness of projects representing a strong combination of capacities and opportunities. This process results in the selection of a TA (or multiple thereof) consisting of a set of projects based on related innovation capacities. The second phase is dedicated to concretise the actions necessary to implement the projects of related innovation capacities identified in the first phase of the workshop in a given region.