This study examines the effect of logistics service quality (LSQ) on customer satisfaction and repurchase intention in e-commerce, focusing on the motorcycle spare parts market. Given the projected growth of e-commerce, LSQ is critical for competitive differentiation. Despite technological advancements, issues like extended transit times, customs delays, and inconsistent service standards often lead to customer dissatisfaction, impacting repurchase intentions. Thus, enhancing overall logistics service quality requires further investigation. A quantitative approach using Structural Equation Modeling (SEM) with AMOS software was utilized to analyze the relationships among web design, return logistics service, responsiveness, information quality, overall LSQ, customer satisfaction, and repurchase intention. Data was collected via online questionnaires from 112 respondents, primarily male (82%) and aged 20–29 (62%), who purchased motorcycle spare parts through e-commerce platforms. Results show that web design, responsiveness, and information quality significantly influence both Overall Logistics Service Quality (OLSQ) and customer satisfaction. OLSQ positively impacts customer satisfaction and repurchase intention. Customer satisfaction, in turn, strongly drives repurchase intention. While return logistics service had a minimal effect on OLSQ, it showed a significant negative relationship with customer satisfaction, highlighting the need for efficient return process management. In conclusion, e-commerce businesses, especially in the spare parts sector, should prioritize improving web design, responsiveness, information quality, and return logistics processes. This focus will enhance LSQ, boost customer satisfaction, and ultimately increase repurchase intentions, crucial for long-term customer loyalty and sustained growth in the competitive e-commerce landscape.