Among the folate compounds, 5-methyltetrahydrofolic acid (5-CH3THF) is regarded as one of the most bioactive forms of folate. It is regarded as the better source of folate to humans as compared to folic acid, a synthetic form of folate, which is used for fortifying foods to prevent the incidence of neural tube defects in the new born babies. The use of 5-CH3THF as an alternative fortificant, in place of folic acid, has been explored by various researchers. However, fortification of 5-CH3THF is problematic due to its lower stability. This study investigated the stability of microencapsulated 5-CH3THF in biscuits baked at various temperatures and times as well as changes in their physical properties. Microcapsule with pectin and alginate ratio of 80:20, prepared by spray drying, gave the highest retention (68.6%) of the 5-CH3THF, therefore, chosen for fortification. The encapsulated and unencapsulated 5-CH3THF were mixed separately with flour and biscuit ingredients and baked at 180℃, 200 and 220℃, each for 5, 9 and 12 min. The inclusion of encapsulated and unencapsulated 5-CH3THF in the biscuit formulation and subsequent baking at various temperatures and times resulted in retention of 5-CH3THF from 19.1% to 1.7%. Microencapsulation of 5-CH3THF slightly improved the retention of 5-CH3THF over unencapsuated biscuits at 180℃ for 5 min, but almost no such effect was achieved under baking temperatures of 200℃ and 220℃. Physical analysis showed darker colour, harder texture and lower moisture content for biscuits baked at higher test temperatures. It seems intense heating condition that caused “over baking” of the biscuit likely to be responsible for the loss of the vitamin as well as less desirable physical properties of the biscuits.