Propolis is a resinous substance known for its bioactive compounds, such as phenolics and flavonoids, which exhibit antioxidant, antibacterial, and anti-inflammatory benefits. While this can be harvested from sources globally, it can also be derived from the native stingless Philippine kiwot bees. This study used microwave-assisted extraction (MAE) using ethanol, changing the solvent-to-sample ratio (5mL/g, 10mL/g, and 15mL/g), solvent concentration (35%v/v, 65%v/v, and 95%v/v), and extraction time (60s, 180s, and 300s), to determine their effects on the yield and phenolic and flavonoid contents. The extracted propolis was concentrated using rotary evaporator and freeze-dried. Phenolic content was determined through Folin–Ciocalteu method, while flavonoid content was identified through aluminum chloride complex formation in methanol solution. Interactions between solvent-to-sample ratio and solvent concentration significantly affected yield, while extraction time did not. Results show that using MAE with ethanol as a solvent successfully extracted propolis. Lower solvent-to-sample ratios with increasing solvent concentration resulted in higher yields. Conversely, high solvent concentrations with increasing solvent-to-sample ratio decreases yield. The highest yield (0.144 g/g) was obtained with 5mL/g solvent-to-sample ratio, 95%v/v solvent concentration, and 300s extraction time. Highest phenolic content (180.145 mgGAE/g propolis) was observed with 5mL/g solvent-to-sample ratio, 95%v/v solvent concentration, and 60s extraction time, while highest flavonoid content (124.190 mg QE/g propolis) was determined with 10mL/g solvent-to-sample ratio, 35%v/v solvent concentration, and 180s extraction time. Effects of extraction parameters were determined, which can further optimize the quantity and quality of propolis.