Digital transformation has become a key factor in increasing the competitiveness of the natural resources sector, especially in developing countries facing efficiency and productivity challenges. This study aims to analyze the influence of digital transformation on business efficiency and organizational productivity, emphasizing the mediating role of efficiency in the context of Indonesia’s natural resources. The research method used is a quantitative approach with the Structural Equation Modeling–Partial Least Squares (SEM-PLS) method on 385 respondents from natural resources companies in East Java. The results show that digital transformation has a significant effect on business efficiency (β = 0.47; p < 0.001) and organizational productivity (β = 0.32; p < 0.001). Efficiency is proven to act as a partial mediator (β = 0.21; p < 0.001), confirming that the main impact of digitalization on productivity is obtained through increasing efficiency first. These findings strengthen the Resource-Based View and Dynamic Capabilities Theory, which proves efficiency as a key mechanism in the context of developing countries’ natural resources. The practical implications of this research demonstrate the need for natural resource companies to prioritize digital investments in energy savings, logistics management, and technology-based monitoring.