San Miguel de Allende is located in the eastern part of GuanajuatoEstate in Mexico’s mountainous bajío region. The bajío (low place) is a relatively flat region about 2,000 m (7,000 ft) above sea level surrounded by mountains; it is a part of the Mexican altiplano. San Miguel serves as the administrative seat for the surrounding municipality of San Miguel de Allende, Guanajuato.

San Miguel de Allende is located at 20°55N 100°45W / 20.917, -100.75.

The municipality rests at 1,870 m (6,140 ft) above sea level. The municipality extends over an area of 1,537.19 km² (593.51 sq mi).

San Miguel is bordered to the North by the municipalities of San Luis de la Paz and Dolores Hidalgo. To the west it is also bordered by Dolores Hidalgo. To the south the municipality is bordered by Juventino Rosas, Guanajuato and Comonfort and to the southeast by Apaseo el Grande. To the northeast it is bordered by San José Iturbide. Finally, to the east it is bordered by Querétaro municipality in the state of Querétaro. The municipal seat is located 274 km (170 mi) from Mexico City and 97 km (60 mi) from the state capital of Guanajuato.