Despite the availability of various tools, practitioners often lack a holistic perspective when conducting sustainability-related improvement activities. Existing Value Stream Mapping (VSM) tools that incorporate environmental aspects suffer from a lack of standardization and limited alignment with sustainability reporting standards. This paper introduces a framework for VSM that integrates sustainability indicators to assess and enhance the triple-bottom-line performance of manufacturing processes aligned with the global reporting initiative (GRI) standards. We validate the proposed framework through a case study conducted in a biopharmaceutical production system of a small and medium-sized enterprise (SME) that employs single-use technologies. The study highlights the critical need for collaboration with equipment suppliers to develop production specifications considering operational performance and environmental impact, thereby capturing a comprehensive perspective. By utilizing the proposed framework, practitioners can identify opportunities for improving the design and efficiency of production systems. The case study provides valuable insights into SMEs’ challenges when transitioning to sustainable production, particularly when product-related requirements impose limitations on sustainability improvements. Although the framework's validation focuses on a biopharmaceutical SME, it can be applied to manufacturing companies across industries to assess and enhance all three aspects of sustainability in their processes.