Background: Developing countries, such as the Philippines, started implementing policies to improve access to medicines, which is a vital step toward universal healthcare coverage. This study aimed to evaluate the prices, availability and affordability of prescribed medicines for diabetes, hypercholesterolemia and hypertension with the exemption of 12% value-added tax in the Philippines. Methods: The prices and availability of 50 medicines were collected in August 2019 from 36 public and 42 private medicine outlets in six regions of the Philippines, following a modified methodology developed by the World Health Organization and Health Action International. Availability is reported as the percentage of outlets in which the surveyed medicine was found at the time of visit. Medicine prices are expressed as median unit prices (MUPs) in Philippine Peso. Affordability is calculated based on the number of days’ wages required for the lowest-paid unskilled government worker to purchase a monthly treatment. Results: The mean availability of surveyed medicines was low in both public and private sectors, with 1.3% for originator brands (OBs) and 25.0% for lowest-priced generics (LPGs) in public outlets, and 34.7% and 35.4% in private outlets, respectively. The MUP of medicines were higher in private outlets, and OBs have higher unit price compared to the generic equivalents. Treatments with OBs were unaffordable, except for gliclazide, but the affordability of most LPGs is generally good. Conclusion: Access to medicines in both sectors was affected by low availability. High prices of OBs influenced the affordability of medicines even with tax exemption. A review of policies and regulations should be initiated for a better access to medicines in the Philippines.