Purpose: New technologies, innovations and sustainable solutions are essential for achieving companies' strategic objectives. Meanwhile, the requirements for efficient allocation of resources to knowledge, innovations and, in particular, research and development (hereinafter only "R&D") are becoming ever more demanding. The aim of this paper is to modify the Balanced Scorecard (hereinafter only "BSC") framework to improve the R&D performance management in a selected company using a case study approach. Design/methodology/approach: Qualitative research methods consisting of a case study and semi-structured interviews were implemented in accordance with a reference framework to fulfilment the paper's aim. Findings: Cooperation and collaboration in the R&D networks is essential for small and medium-sized enterprises (hereinafter only "SMEs") to achieve the required financial performance. This paper suggests a BSC framework for R&D management in the case company that respects both the business character and also the strategic objectives and priorities of the selected company. Research/practical implications: This paper is delivering recommendations how to manage R&D performance with a respect to the character of business activity and strategic objectives. This paper is also offering recommendations on managing R&D activities using the example of a SME conducting bio-economy-related R&D activities. Originality/value: Expanding population and production create growing pressure on biological resources the consumption of which is already pressing capacity limits. With new challenges, demands on R&D management systems are ever-increasing. At company level, a current challenge for managers is to choose an adequate R&D management methods.