Context: Scientific research, increasingly reliant on data and computational analysis, confronts the challenge of integrating collaboration and data sharing across disciplines. Collaborative frameworks that support decentralized decision-making and knowledge-sharing are essential, yet integrating them into computational environments presents technical challenges, such as decentralized identity, user-centered policy-making, flexible asset management, automated provenance, and distributed collaborative workflow management. Solution: This study introduces a conceptual framework and its prototype implementation called Decentralized Virtual Research Environment (D-VRE). This approach enhances seamless, trusted data sharing and collaboration within research lifecycles. It incorporates custom sharing policies, secure asset management, collaborative workflows, and research activity tracking, all without centralized oversight. Evaluation: Demonstrated through a real-world case study in the CLARIFY project, the prototype of the decentralized virtual research environment proved effective in enabling advanced data sharing and collaborative scenarios, showcasing its adaptability in scientific research. Results: Integrated into JupyterLab, D-VRE supports custom collaboration agreements and smart contract-based automated execution on the Ethereum blockchain. This ensures secure, verifiable transactions and promotes trust and reliability in shared research findings. Contribution: D-VRE addresses barriers to scientific research collaboration and data sharing, offering a scalable and adaptable decentralized model. This model promotes a more inclusive, efficient, and trustworthy research ecosystem, paving the way for future advancements in virtual research environments.