E-commerce search optimization has evolved to include a wider range of metrics that reflect user engagement and business objectives. Modern search frameworks now incorporate advanced quality features, such as sales counts and document-query relevance, to better align search results with these goals. Traditional methods typically focus on click-through rate (CTR) as a measure of engagement or relevance, but this can miss true purchase intent, creating a gap between user interest and actual conversions. Joint training with the click-through conversion rate (CTCVR) has become essential for understanding buying behavior, although its sparsity poses challenges for reliable optimization. This study presents MOHPER, a Multi-Objective Hyperparameter Optimization framework for E-commerce Retrieval systems. Utilizing Bayesian optimization and sampling, it jointly optimizes both CTR, CTCVR, and relevant objectives, focusing on engagement and conversion of the users. In addition, to improve the selection of the best configuration from multi-objective optimization, we suggest advanced methods for hyperparameter selection, including a meta-configuration voting strategy and a cumulative training approach that leverages prior optimal configurations, to improve speeds of training and efficiency. Currently deployed in a live setting, our proposed framework substantiates its practical efficacy in achieving a balanced optimization that aligns with both user satisfaction and revenue goals.