This chapter presents a systematic analysis framework for design operability and retrofit of energy systems. This analysis framework consists of Disruption Scenario Analysis (DSA), Feasible Operating Range Analysis (FORA) and debottlenecking analysis for an energy system design. In the proposed DSA, equipment failure scenarios are examined to determine the operability of an energy system design. Meanwhile, FORA determines the feasible operating range of an energy system, taking into account the interdependency between utilities produced and represents a range of net utility output that can be delivered within design and performance limitations. Such range allows designers to determine whether an operating energy system requires debottlenecking and retrofitting. In the event where debottlenecking of an existing energy system is required, the proposed framework incorporates step-by-step debottlenecking procedures. To illustrate the proposed framework, biomass energy system (BES) design is used as a illustrative case study. In the case study, the BES is analyzed to determine if it would require retrofitting in order to increase its heat production to 1.5 MW. Based on the results from the analysis, it is found that additonal 50% and 100% increase in anaerobic digester and fired-tube boiler capacity respectively are required. This addiotional capacities yield a favorable benefit-cost ratio (BCR) value of 1.95 which indicates that the benefits from increased heat production is greater than the costs of increasing equipment capacities, hence, making this a viable retrofit action.