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• Identified Blockchain implementation challenges are grouped into five main categories. • A two-phase fuzzy Delphi method is applied for challenges identification. • Fuzzy group-based BWM has been used to prioritize the considered challenges. • Various practical managerial insights are presented based on the results obtained. Blockchain as the trust‐enabling technology has supported and transformed cyber-physical systems in recent years. Therefore, many organizations have adopted blockchain-based technology to develop industrial software-product-service systems. However, the implementation of blockchain at the organizational levels can be related with several technical, organizational, legal, financial, and environmental challenges (intra-organizational and inter-organizational). Analysis of these challenges will play a significant role in organizational performance. This study has investigated an extensive list of challenges of software blockchain-based implementation in cyber-physical systems. The proposed comprehensive model is applied to the software development industry in Iran as a case study. Based on the experts' opinions, challenge identification was conducted via the two-phase fuzzy Delphi method for medium and large organizations. Extensive quantitative and qualitative challenges are evaluated via the efficient best-worst fuzzy method. Obtained results indicate that smart contracts vulnerabilities and deterministic execution of the technical challenge group have the most critical importance and governance of the legal challenge group has the least vital importance. It is mentionable that most technical challenges have higher priority than other considered challenges. [Display omitted] [ABSTRACT FROM AUTHOR]