Medicinal plants have long been used to treat various diseases in both indigenous and non-indigenous populations of Mindanao, Philippines. Here, we extracted data from ethnobotanical studies to compile a comprehensive list of these medicinal plants and identify how and for what purpose they are most commonly used. We identified 530 verified medicinal plant species across 372 genera in 118 families. The two most frequently cited species were and . The most represented family was Fabaceae and the most represented genus was . A total of 28 medicinal plant species are designated as threatened at the national or global level; of these, 11 are endemic to the Philippines. Medicinal plant preparations most commonly use leaves for oral administration to treat various diseases such as digestive issues, including diarrhea. This study underscores the need for further ethnobotanical investigations, particularly in areas lacking records. It also emphasizes the need for conservation of threatened and endemic medicinal plants to ensure sustainable utilization of this valuable resource.