<p>Pakistan is currently facing significant challenges in meeting the food and energy needs of the country. Sustainable agricultural production can help in meeting these challenges. Food and energy are closely interlinked in agricultural production systems, as agriculture is consumer as well as producer of energy. To investigate the food-energy nexus, this study analyzes the yield performances and energy efficiencies of wheat, rice and cotton cropping systems of Punjab and Sindh. The yield analysis was conducted by applying a stochastic model and energy analysis using indicator based approach. Findings of the study indicate hotspots that have lower crops yields, declining yields, larger yield gaps indicating an unsustainable use of the input resources and gives insights on inter and intra provisional comparison of the yield performance and energy efficiency. Almost 84–93% of energy used for crop production came from non-renewable sources. Cotton crop in Punjab and rice crop in Sindh have not performed well in past four decades. Use of non-renewable energy sources, inorganic fertilizers, conventional management practices, burning of crops residue are prevailing in the study area. By assessing the analysis outcomes, this study draws the implications for food security and agricultural sustainability and suggests measures to achieve them in the study area.</p>