Abstract Background The evidence-base for whole school approaches aimed at improving student mental health and wellbeing remains limited. This may be due to a focus on developing and evaluating de-novo, research-led interventions, while neglecting the potential of local, contextually-relevant innovation that has demonstrated acceptability and feasibility. This study reports a novel approach to modelling and refining the programme theory of a whole-school restorative approach, alongside plans to scale up through a national educational infrastructure in order to support robust scientific evaluation. Methods A pragmatic formative process evaluation was conducted of a routinized whole-school restorative approach aimed at improving student mental health and wellbeing in Wales. Results The study reports the six phases of the pragmatic formative process evaluation. These are: 1) identification of innovative local practice; 2) scoping review of evidence-base to identify potential programme theory; outcomes; and contextual characteristics that influence implementation; 3) establishment of a Transdisciplinary Action Research (TDAR) group; 4) co-production and confirmation of an initial programme theory with stakeholders; 5) planning to optimise intervention delivery in local contexts; and 6) planning for feasibility and outcome evaluation. The phases of this model may be iterative and not necessarily sequential. Conclusions Formative, pragmatic process evaluations can support researchers, policy-makers and practitioners in developing robust scientific evidence-bases for acceptable and feasible local innovations that do not already have a clear evidence base. The case of a whole-school restorative approach provides a case example of how such an evaluation may be undertaken.