Background The nominal group technique has been shown to be an effective method for reaching consensus among a group of healthcare experts when selecting clinical indicators for application in primary care research, especially where there are competing prioritisation criteria being considered. In the context of manifest barriers to traditional face-to-face meetings, and with the advent of evolving and improved digital tools, alternative approaches are being more commonly utilised to overcome these challenges. In this study, we sought to prioritise a set of existing, validated clinical indicators proposed for inclusion in ACTMed (ACTivating primary care for MEDicine safety), a clinical trial aiming to reduce medicine-related harm in primary care. Methods A modified nominal group technique, using a fully online approach, was employed to facilitate consensus among a group of pharmacists and general practitioners. Quantitative data were obtained using an online survey platform both prior to the structured virtual forum and again following group discussion. Qualitative material was gathered from written feedback included in the pre-forum questionnaire and through verbal contributions made during the online forum. Results The highest priority indicators determined by the two-staged survey process were for myocardial ischaemia, cerebrovascular ischaemia related to atrial fibrillation, heart failure, asthma/chronic obstructive pulmonary disease and falls with fracture. Qualitative reasoning behind the participants’ evaluation of the clinical indicators included value for money, impact of the intervention, consequences of clinical outcomes and ability to implement the intervention in practice. Conclusions In this study, the interactive component of the nominal group technique process had little impact on the final prioritisation of the clinical indicators. Potential explanations for this might include previously established strong participant views and preferences or relative group homogeneity based on similar learning, research or clinical experience.