During this time, he also joined with civilian groups in investigating Indian attacks and married Victoria Zaff in 1869. The couple would have two children.

By 1871, he was made the sheriff of Yavapai County, a position he held for two years. In 1873, he was the Prescott representative in the Seventh state assembly. In 1875, he and his wife divorced and Behan moved to Mohave County, where once again he was a state assembly representative, this time for Mohave County in 1879.

When mining in Tombstone began, he moved south and in 1880, became a deputy under Sheriff Charles A. Shibell of Pima County. When Cochise County, which included Tombstone, was organized in 1881, Behan became its first sheriff. Working for him as deputies were Frank Stilwell, William Breakenridge, Harry Woods, W.I. Perry, Bill Soule, H.L. Goodman and others.

Shortly after Behan became sheriff, Virgil Earp became the city marshal of Tombstone and recruited brothers Wyatt and Morgan as "special deputy policemen." The Earps almost immediately came into conflict with the Clantons and the McLaurys, to whom Behan was an advocate. This naturally pitted him against the Earps. Adding further fuel to the fire, was Behan's interest in Josephine Sarah Marcus, who was quickly becoming enamored with Wyatt Earp.

After the gunfight at the O.K. Corral on October 26, 1881, Behan arrested Virgil, Wyatt, and Morgan Earp, as well as Doc Holliday for the murder of Billy Clanton, Tom McLaury and Frank McLaury. However, the judge decided that the Earps and Holliday had been justified in their actions.

In September, 1882, after the Earp Vendetta Ride, Behan had a feud with his own deputy, William Breakenridge, which made him unpopular with Cochise County citizens. At the same time, investigations discovered that Behan had somehow banked some $5,000 during his tenure as sheriff. Where the money came from was never discovered.

In the end, public criticism of Behan resulted in his showing last on the ballot of possible sheriff nominees for his own party, an unusual result for a seated sheriff. Losing the nomination, he was forced out of office in November, 1882.  He would never serve as a peace officer again.