Purpose The Iranian bio-pharma industry was the first high-tech industry in the country, which had succeeded to develop innovative products. Despite past successes, there are bottlenecks preventing the industry from meeting the national standard and plans for excellence. The purpose of this paper is to find out the challenges impeding further innovation of the firms in the industry and find solution to the issues. Based on these findings, the authors recommend a set of policies that might be of interest to the new-comer countries in biotechnology. Design/methodology/approach The institutional structure of the industry, its market situation and the players are studied using a qualitative method based on an institutional approach and an appreciative theory. Findings Ten challenges were found after examining the pyramid of technological capabilities. Moreover; conflicting approaches in the policies made for the national health system and industrial development are identified. Adoption of policy coherence has been highlighted as a necessary strategy to harmonize and integrate the approaches required to play a role in bio-production global market actively. Practical implications A unique focal point for the country’s strategic plans should be assigned, and the supply-side policies with demand-side policies must be balanced. Originality/value This paper is an evidence-based effort to bring policy coherence as an approach in sectoral level, while political settlement lies in governance level. The opportunities for improvement are highlighted in the Iranian bio-pharmaceutical sector, as a key technology. Moreover, the findings could be used as lessons-learned for new-comers countries.