In 1760 the master builder of Bidstrup Manor died and Mørup was tasked with finishing the project. The following year he designed an extension for Aarhus Cathedral School which is today known as the White Building. The extension was extensively altered in 1847 when it was given an additional floor and a neoclassical appearance. In 1780 Mørup built Randers City hall which may be his best known work and which was protected as a listed building in 1918.
Christian Jensen Mørup worked in a dated Baroque style with some newer elements such as the lesene-arch framing the porch portal in Bidstrup Church which can be found in all his later works. Randers City Hall also has elements thought to be inspired by works by Niels Eigtved.