Passengers’ perceptions of transit quality depend on their interactions with the service. However, given the varied operational features in any transit network, the perceived service quality is expected to vary between different types of operation. Recently, there has been an emphasis on addressing this issue and quantifying the variation in the perceived service quality at route level. In this respect, this study quantifies the perceived quality of bus services across different route types and user groups. A two-step cluster analysis is developed to classify bus routes based on their operational features, which is followed by a series of importance-performance analysis (IPA) models corresponding to each route type. The study is supported by a primary dataset collected from 1,883 users through an online survey in Hamilton, Canada. The emerging results indicate four predominant route types: core, standard, express, and local routes, each exhibiting a unique set of characteristics. The IPA models show an apparent variation in the perceived service quality from each route-type. In addition, there are clear indications of differential perception between passengers who use the service very frequently and other less frequent users. These results call for the consideration of variations in route level and user type in informing service quality improvements.