The competition of e-commerce in Indonesia makes domestic and foreign e-commerce companies plan strategies to win the competition. Customer’s loyalty is an important factor to lead in the competition. This research focuses on how much influence of the website quality on customer’s loyalty. This study also finds out which factor of website quality has the most influence on customer’s loyalty with customer’s satisfaction as a mediating factor. Factors that influence e-commerce customer’s loyalty were analysed using the WebQual4.0 method which consists of three dimensions. The samples used in this research were 400 respondents. The data analysis techniques used were Structural Equational Model (SEM) using version 3.0 SmartPLS and Importance and Performance Map Analysis (IPMA). The analysis of SEM showed that the information quality was the only one that had a positive and significant influence on customer’s satisfaction and loyalty on the JD.id website, while the usability and service factors had no positive and significant effect. The analysis of IPMA showed that the performances that should be improved were the maintenance of accurate and detailed information and content development.