On 1 October 1982, he became Landesbischof of the Lutheran Church in Brunswick, with its seat in Wolfenbüttel, serving until 31 May 1994.[2][3] He focused on the spiritual care of pastors and their families.[3] Faced with rising numbers of people leaving the church, he supported projects seeking more intense contact with members such as the missionary "Neu anfangen".[3][2] He contacted also influential people outside the church such as mayors, managers and scientists. After German reunification, two parishes, Blankenburg and Calvörde, were returned into the Brunswick Church in 1992. Müller had visited Blankenburg immediately when the border was opened, to establish contact.[3] During his tenure as bishop, he taught church history at the Göttingen University.[3]
From 1990 to 1993, Müller also served as Leading Bishop (German: Leitender Bischof) of the United Lutheran Church of Germany, after three years as vice bishop.[3]