An 1867 Supreme Court ruling designated Waukon as the seat of Allamakee County, officially ending a fifteen year county seat controversy. In 1851, voters selected now-deserted Columbus as the county seat; two years later, voters changed course and designated Waukon as the seat, and confirmed this decision in a 1859 vote. While a new courthouse was constructed in Waukon in 1861, residents voted to assign county seat status to Lansing the following year. In 1864, the county sheriff and his Waukon-based posse attempted to steal the county records, but the effort was intercepted and the records were returned.

Following the Supreme Court decision, the 1861 building served as the county courthouse until 1940, when a new, larger facility was constructed. The historic building now serves as the Allamakee County Historical Museum, which has a number of local artifacts. The original second-floor courtroom is intact and open to the public during museum hours.