Since 1791, the departmental capital had been the seat of the constitutional bishopric of the Upper Rhine. Colmar had its own bishop and St. Martin´s church was able to claim cathedral status. Less than ten years later, the prefect set up office in Colmar for the first time, thereby bolstering Colmar´s position as administrative capital. The Upper Rhine department began to grow. It already included the city of Belfort and its territory, and it was also to acquire the department of Mont Terrible, followed in 1800 by the former principality of Porrentruy, Erguel, the provostship of Moutier Granval et Bellay and part of the former principality of Montbéliard, which would remain in Alsace until 1815.
The first Prefect of the Upper Rhine was Jean-Baptiste Harmand, who came from the Meuse and failed to make much of an impression in Colmar. It should be said that he did not really have time on his side as he only lasted eight months in the job before being recalled to Paris after being caught "in a scandalous conflict with his general secretary". The next mention of Harmand showed him to be French consul in Santander, Spain. Dismissed during the one-hundred-day period (the hundred days when Napoleon retook power in 1815), he finished up living in poverty under the Restoration. He was known as a "political chameleon", although this description also concerned any of his contemporaries. Political twisting were spectacular between the Revolution and the Restoration.
The prefecture itself was set up in the old abbey of Pairis, the then Town Hall, in 1800. In the same year, Colmar once again became the judicial capital of Alsace and was made the seat of the Appeal Tribunal (tribunal d´appel), which became an Appeal Court (Cour d´appel) in 1804 and then an Imperial Court in 1810. In April 1800, every French commune found itself headed by a Mayor, after the title had been restored following Napoleon´s coup d´état. The new Mayor of Colmar was François Antoine Richter. He worked under the Prefect, Félix Desportes, who would remain in the job from 1802 to 1813 before being thrown out for misappropriating public funds. Between the two of them they helped the city expand beyond its walls. The old city gates were knocked down, which earned the prefect the nickname "gate destroyer". The Champ de Mars military exercise field was changed into a public park. The unfortunate Harmand was credited with producing the original plans for the alleys and shrubs and trees, which were designed in the shape of the Légion d´honneur.