On July 28, 2006, the Nationals acquired Martis from the San Francisco Giants for veteran leftyrelieverMike Stanton. He joined the roster of Savannah of the South Atlantic League on August 1, 2006. After going 1–1 with a 3.80 ERA in four starts at Savannah, Martis was promoted to Washington's Potomac club in the High A Carolina League. He pitched two games in Potomac, giving up 4 earned runs in 12 innings, and finished the season at Harrisburg in the Double-A Eastern League, allowing 7 earned runs over 5 innings in his only appearance of the Harrisburg season. In 2007, Martis pitched for Potomac the entire season. In 26 starts and one relief appearance, he logged a 4.23 ERA over 151 innings, striking out 108 batters while issuing just 52 walks. Martis was assigned to Harrisburg to begin the 2008 season. After going 4–4 with a 3.98 ERA and a respectable 1.35 WHIP in 14 starts at Harrisburg, he was promoted on June 21 to Triple-A Columbus, where he went 1–2 and accrued a 3.02 ERA in 7 starts, striking out 42 batters and walking 17. He was selected as a member of the World Team for the 2008 All-Star Futures Game in Yankee Stadium. Martis was called up to the major-league roster on September 2, with the intent of assigning him to the bullpen. However, an injury to rotation member Collin Balester caused Martis to put into the starting rotation. He made his major league debut September 4, 2008, against the Atlanta Braves. He gave up 2 runs in 5 innings, getting the loss. He struck out the first batter he faced, Gregor Blanco. Chipper Jones got the first hit off Martis. In his first plate appearance, he drew a walk from Braves rookie James Parr, who, like Martis, was also making his first major-league appearance. Martis struck out Parr in Parr's first at-bat earlier in the game. Martis got his first major league win on September 23, 2008, against the Florida Marlins. On May 2, 2009, against the St. Louis Cardinals, Martis pitched his first career complete game, which was the Nationals' first complete game since Pedro Astacio's in 2006 against the Atlanta Braves.
In June 2012, Minnesota Twins acquired Martis from the Pittsburgh Pirates for a player to be named later or cash. In 9.2 innings he struck out 7, working to a 5.59 ERA. Martis was outrighted off the roster on October 2, 2013.