The present invention relates to a process of preparing a pharmaceutical composition of metformin and linagliptin or salt thereof. In particular, the present invention relates to a process of preparing stable oral pharmaceutical composition comprising fixed dose combination of metformin and linagliptin or salt thereof. By using an amino sugar, it is possible to achieve the stable pharmaceutical composition of metformin and linagliptin. The invention further relates to use of such composition in the treatment of diabetes mellitus.