Microencapsulation of model drug, acetylsalicylic acid into bio-based polymer, alginate-pectin matrix has been undertaken in this work to characterize the microcapsules based on their composition. Different proportions of the alginate-pectin solutions prepared with drug were homogenized and atomized using nitrogen gas into 1.0M calcium chloride solution to form sol-gel microcapsules. Drug loaded microcapsules were dried using microwave energy under vacuum at low temperature. Average particle size of the microcapsules was found to be 90 micron. Scanning electron microscopy graphs and Fourier Transform Infrared Spectroscopy analysis on the microcapsules confirm the presence of drug in the polymer matrix. X-ray diffraction pattern showed that the microstructure was more like an amorphous pattern. Drug release of the microcapsules was tested in three different pH levels of 1.2, 7.4 and 8.2. Slow and controlled release of drug was observed at all the pH levels. Increase in pectin increased the drug release and also the release was more in acidic pH ( 1.2) as 75.6% for alginate: pectin-20:80.