Bowen was one of the most controversial mayors in the history of the American capital, because of his outspoken support of emancipation and racial integration. to begin business as a merchant. President James K. Polk appointed Bowen to a clerkship in the Treasury Department in 1845, but revoked the appointment three years later when Bowen gained the reputation of a radical for distributing abolitionist propaganda. Additionally, he supported Freesoil candidate Martin Van Buren in that year"s presidential election rather than Polk"s preferred successor, Lewis Cass.
Upon his inauguration as President in 1861, Abraham Lincoln appointed Bowen as Police Commissioner for the District of Columbia, beginning the latter"s career in city politics.
The following year he became Tax Collector for the District, and in 1863 was appointed the District of Columbia postmaster. In 1868, Bowen was nominated by the Republicans as a candidate for Mayor of Washington against Democrat John T. Given.
At that time, post-Civil War Washington had been ravaged by the war and by a desperate shortage of funds from Congress. The city had deteriorated so badly that there was much talk in the Federal sector of relocating the seat of government to Saint Louis.
Bowen ran for mayor under the slogan "A vote for Bowen is a vote for keeping the capital in Washington." In that year"s July election, blacks voted in Washington for the first time, and because of Bowen"s famous support of civil rights, he received narrow support from white voters and overwhelming support from black ones.
Once elected, however, Bowen"s activism startled even the Radical Republican contingent that then dominated Congress. He agitated for complete integration of the city"s public school system. When that failed, he turned instead to constructing a network of schools specifically for "persons of color," diverting large sums of city funds and even providing $20,000 of his own.
Bowen"s policies of activism on behalf of black civil rights outraged well-to-do white citizens of Washington, but even the Republicans who had enforced black rights and suffrage in the capital concluded that Bowen was far more interested in civil rights for blacks than in governing the city and administering public services.
He spent extravagant portions of the city budget in creating schools and employment for blacks, which, while regarded as noble by the Republicans, drained the coffers of money that was intended for maintaining the city. Bowen was even charged with reducing street service to men using penknives to cut the grass between the cobblestones on Pennsylvania Avenue.
By 1870, the city"s debt had increased by 33 percent over its total two years before. Bowen was universally blamed, enough so that his furniture was seized in a judgement to try to replenish Washington"s funds.
He died in 1896 and was interred at Congressional Cemetery.
After leaving office, Bowen served as president of the Freedmen’s Aid Society, and as a member of the board of trustees of colored schools of Washington and Georgetown the board of school commissioners.