The implementation of lockdown due to the COVID-19 pandemic has affected most businesses worldwide. The transportation business, specifically in the Philippines, has been heavily affected since only the healthcare and essential workers were allowed to leave their homes during the early stage of the pandemic. This paper aimed to explore the service quality of Public Utility Vehicles (PUV) in the Philippines during the COVID-19 pandemic utilizing the SERVQUAL dimensions. A total of 564 participants answered an online questionnaire using the convenience sampling approach, consisting of 58 questions. Structural equation modelling (SEM) was applied to derive the causal relationships between SERVQUAL dimensions, COVID-19 safety protocol, and customer satisfaction simultaneously. Out of the six dimensions, the SEM indicated that COVID-19 protocols, tangibility, and assurance variables were found to significantly affect PUV service quality and thus, customer satisfaction. This study is one of the first complete studies that analyzed the PUV service quality during the COVID-19 pandemic. The findings could provide the government with an evaluation of the compliance of PUVs to the imposed COVID-19 protocols. Furthermore, the framework of this study could also be applied and extended in evaluating PUV worldwide.