The article presents an original methodology for adapting organizational management mechanisms during the launch of Agile units as part of digital transformation. The methodology addresses key limitations of traditional management, including rigid budgeting, non-adaptive support functions, long-term contractor agreements, and insufficient performance monitoring. Based on real-world cases from digital transformations in the banking sector of the CIS region, the paper justifies the need to adjust governance practices to support the speed, flexibility, and scalability of Agile teams. Core components of the methodology are described, including hierarchical budgeting, integrated support functions, flexible contractor collaboration models, and a comprehensive performance measurement system. The effectiveness of the methodology is supported by empirical data and stakeholder feedback. Potential directions for further research in scaling Agile within traditional large organizations are also outlined.