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The Russian economy faces an imperative to enhance national competitiveness as a prerequisite for maintaining socio-economic security. The Strategy for Scientific and Technological Development of the Russian Federation (STR Strategy) is conceived as a long-term framework aimed at ensuring the country’s sustainable, dynamic, and balanced advancement toward global competitiveness. Although the strategic directions articulated within the STR formally reflect the conceptual principles of the knowledge economy, they lack concrete mechanisms for stakeholder interaction, the realization of which is essential for achieving the strategic objectives of socio-economic development across all levels of governance. Since the inception of the STR Strategy, the conceptual model for managing the economic development of the Russian Federation within the paradigm of a knowledge-based economy has remained insufficiently defined. In this regard, the primary objective of the present study is to substantiate a methodological framework for constructing an evaluation system that measures the effectiveness of managing the economic development of socio-economic systems in the context of a knowledge economy. The research methodology is grounded in the dialectical, systemic, deductive, indicative, and synergetic approaches, which together provide a comprehensive analytical basis for examining the dynamic interrelations among innovation, competitiveness, and socioeconomic stability. The scientific novelty of the study lies in the development of theoretical propositions, methodological guidelines, and practical instruments for the organization of monitoring systems aimed at evaluating the innovative potential of socio-economic systems at multiple hierarchical levels. The study synthesizes interdisciplinary theoretical foundations concerning the nature and mechanisms of ensuring national competitiveness within a knowledge-based economy. The research design employs a deductive approach encompassing four analytical levels: cross-country comparison, national scale, regional level, and organizational level. Using R. Solow’s model of economic growth as an analytical framework, the paper examines key determinants of global economic development and establishes that the total factor productivity (TFP) exerts a decisive influence on Russia’s economic performance. The analysis identifies regions of the Russian Federation exhibiting structural weaknesses in socio-economic development and empirically confirms the dependence of regional socio-economic security on the degree of innovative activity within organizations. The proposed analytical toolkit provides a foundation for information and analytical support in assessing the contribution of organizational innovation to the effectiveness of socio-economic systems at various levels of aggregation. Future research should focus on elaborating a comprehensive mechanism for managing national socio-economic security within the institutional framework of the knowledge economy, thereby enhancing the strategic resilience and global competitiveness of the Russian Federation.