 Denkendorf is first mentioned in a document of 1129 in which Pope Honorius II took the monastery of Denkendorf under his protection.During the construction of the Autobahn (A8 today) in 1935, a series of Alemannic burial sites was uncovered, which are dated in the period shortly before 700 A.D.

After the end of World War II, the population soared, quadrupling from 1945 to 1995.Despite the district and municipal reform of 1973/74 Denkendorf maintained its independence.