The retrofitting of buildings for improved energy efficiency has been recognized as crucial for achieving climate mitigation goals in Bosnia and Herzegovina (B&H). However, performing multi-objective optimizations for retrofitting existing buildings poses challenges, as it requires balancing conflicting objectives such as retrofit costs, energy savings, and CO2 reduction. To tackle this challenge, we employed a multi-objective analysis approach that aims to identify Pareto-optimal solutions for retrofitting, striking a balance between energy consumption, CO2 emissions, and retrofit costs. In this study, we utilized a combination of Full Factorial Design (FFD) and the state-of-the-art NSGA-III framework to evaluate energy-efficient (EE) retrofit strategies for residential buildings in B&H. The analysis was based on the existing building database from the national TABULA study, serving as a fundamental reference. By analyzing this data, we aimed to determine the optimal approach for EE retrofitting in single-family homes (SFH). Key results indicate that upgrading external walls and improving heating system efficiency are the most effective measures for reducing energy consumption and CO2 emissions. However, these measures come with higher retrofit costs. A multi-objective optimization approach identifies a set of non-dominated solutions representing energy efficiency retrofit measures with the lowest specific final energy for heating, specific CO2 emissions, and overall retrofit costs. The top-ranked set of measures achieves a Simple Payback Period (SPP) of 19.9 years. The insights gained from this study are intended to provide valuable guidance to decision-makers in formulating cost-effective and energy-efficient retrofitting strategies that simultaneously minimize annual energy consumption, CO2 emissions, and retrofit costs.