Molony was elected as a Democrat to the 32nd United States Congress (March 4, 1851-March 3, 1853). He was not a candidate for renomination in 1852. He moved to Humboldt, Nebraska, and engaged in agricultural pursuits 1866-1891. In 1882 he declined the Democratic nomination for United States Senator from Nebraska on account of ill health. He was again a delegate to the Democratic National Convention at Chicago in 1884. He died in Humboldt, Nebraska, December 14, 1891. He was interred in Belvidere Cemetery, Belvidere, Illinois.