Muslims worship together more frequently than members of other religions. They pray in congregation at the mosque five times a day, causing the mosque to become a central hub for COVID-19 transmission. Therefore, the adoption of protective measures as a method of mitigating the COVID-19 pandemic in mosques is vital. This study aims to account for the implementation status of protective measures in mosques in Surakarta City, Indonesia, during the COVID-19 pandemic. A cross-sectional survey was conducted using a structured questionnaire sent to mosque caretakers as research participants. The mosques were chosen using a simple random sampling technique for a total sample of 247 mosques in Surakarta City. Participants were asked how often they implement the following protective measures in mosques, as recommended by the Majelis Ulama Indonesia: checking body temperature before entering the mosque, prayer distancing, carrying own prayer mat, wearing a mask when praying and no handshaking after prayer. The prevalence of the adoption of protective measures was revealed to be amongst 44.6% to 92.6%, with the lowest prevalence in checking body temperature before entering the mosque. Overall, only 33.7% of mosques implemented all protective measures. In mosques affiliated with Nahdlatul Ulama and the small mosques, the prevalence of protective measures was lower than in mosques affiliated with Muhammadiyah and the large mosques, respectively, suggesting that it is crucial to develop targeted health messages for these groups. Finally, as religious communities remain active in congregational worship during the outbreak, the contradictions between medical and religious practices must be addressed in society for believers to adopt public health policies and for policymakers to comprehend the importance of religious observances.