The current work is focused on the solubility and catalytic behaviour of K2CO3, and Na2CO3 during the synthesis of biodiesel from Calophyllum Inophyllum oil (CIO) in methanol. The solubility of K2CO3, and Na2CO3 in methanol is not straight forward, as both form their respective methoxides and bicarbonates on solubility in methanol. Therefore to understand catalytic behaviour of both carbonates, it is essential to estimate sodium and potassium methoxides, and bicarbonates formed at different temperatures. In this regard, the catalytic behaviour of both carbonates was studied between 50 °C to 65 °C. Therefore, solubility behaviour of both carbonates explored during the synthesis of biodiesel from CIO by transesterification process. At higher temperature, the concentration of potassium and sodium methoxides decreased and their bicarbonate concentration increased. This solubility behaviour found to be more useful to differentiate homogeneous and heterogeneous catalytic route for biodiesel synthesis. At higher temperature, 65 °C, K2CO3, and Na2CO3 exhibited heterogeneous catalytic behaviour, but Na2CO3 showed relatively higher heterogeneous catalytic behaviour as it form higher concentration of insoluble sodium bicarbonate. Therefore, Na2CO3 could be a better heterogeneous catalyst for biodiesel synthesis at higher temperatures, 65 °C, as it produces low concentration of sodium methoxide which is an advantage from post biodiesel treatment standpoint.