Background: In the Philippines, various mobile health apps were implemented during the COVID-19 pandemic with very little knowledge in terms of their quality. The aims of this paper were 1) to systemically search for mobile apps with COVID-19 pandemic use case that are implemented in the Philippines; 2) to assess the apps using Mobile App Rating Scale (MARS); and 3) to identify the critical points for future improvements of these apps. Methods: To identify existing mobile applications with COVID-19 pandemic use case employed in the Philippines, Google Play and Apple App Stores were systematically searched. Further search was conducted using the Google Search. Data were extracted from the app web store profile and apps were categorized according to use cases. Mobile apps that met the inclusion criteria were independently assessed and scored by two researchers using the MARS-a 23-item, expert-based rating scale for assessing the quality of mHealth applications. Results: A total of 27 apps were identified and assessed using MARS. The majority of the apps are designed for managing exposure to COVID-19 and for promoting health monitoring. The overall MARS score of all the apps is 3.62 points (SD 0.7), with a maximum score of 4.7 for an app used for telehealth and a minimum of 2.3 for a COVID-19 health declaration app. The majority (n = 19, 70%) of the apps are equal to or exceeded the minimum "acceptable" MARS score of 3.0. Looking at the categories, the apps for raising awareness received the highest MARS score of 4.58 (SD 0.03) while those designed for managing exposure to COVID-19 received the lowest mean score of 3.06 (SD 0.6). Conclusions: There is a heterogenous quality of mHealth apps implemented during the COVID-19 pandemic in the Philippines. The study also identified areas to better improve the tools. Considering that mHealth is expected to be an integral part of the healthcare system post-pandemic, the results warrant better policies and guidance in the development and implementation to ensure quality across the board and as a result, positively impact health outcomes. Supplementary Information: The online version contains supplementary material available at 10.1186/s44247-023-00007-2.