Plastic packaging dominates global markets, but its persistence and exponential production have made petroleum-plastic waste an urgent environmental problem. Biodegradable films from agricultural waste are a promising alternative; pectin, abundant in citrus peel, is a candidate biopolymer, yet on its own it forms weak, gel-like layers with poor film-forming ability, and conventional acid extraction is slow and energy-intensive. This study valorizes calamansi (Citrofortunella microcarpa) peel waste—a heavily generated byproduct in the Philippines—by extracting pectin via greener microwave-assisted extraction (MAE) and blending it with chitosan to form biodegradable films. MAE was optimized across pH (1, 1.5, 2) and microwave power (600–800 W), and films were cast at chitosan:pectin (Ch:P) ratios of 25:75, 50:50, and 75:25 and tested for moisture content, swelling, water solubility, biodegradability, and tensile behavior. Pectin yield peaked at 23.62% (pH 1.5, 700 W), with acidic conditions favoring extraction by keeping carboxyl groups protonated, and yields declining at 800 W due to thermal degradation; FTIR confirmed the extracted pectin closely matched commercial pectin. Film properties tracked the balance between chitosan's protonated amine groups and pectin's carboxylate groups. The 50:50 blend maximized ionic crosslinking, giving the lowest swelling and highest tensile strength (3.57 MPa); the chitosan-rich 75:25 film gave the highest moisture retention (19.79%) and lowest solubility (1.19%); and the pectin-rich 25:75 film was most extensible (105.74% strain) and most biodegradable (27.72% mass loss after 10-day soil burial). These results show that chitosan–pectin polyelectrolyte complexation can be tuned through blend ratio to target specific packaging requirements, establishing calamansi-derived films as a viable route to waste-based sustainable packaging.