Koenen signed a two-year free agent contract with the Atlanta Falcons on April 26, 2005. He went on to edge out veteran punter Toby Gowin, who had also signed a free agent deal that offseason, for the starting job with the Falcons. He appeared in all sixteen regular season games for the Falcons, punting 78 times for 3,300 yards, which was good for a 42.3 yards per punt average and ninth in the NFC. He also served as the team's kickoff specialist and was seventh in the NFC in yards per kickoff. His 14 touchbacks put him behind only Pro Bowler Neil Rackers.