In an exchange of players out of minor league options, Andino was traded to the Baltimore Orioles for Hayden Penn on April 1, 2009. He made his first appearance for the Orioles on April 9,, pinch-hitting for César Izturis. He made a barehanded catch of a Justin Morneau pop fly in foul territory during the sixth inning of a 6-1 win over the Minnesota Twins at Target Field on August 24, 2011. He had slightly overrun the ball while approaching the tarpaulin roll parked against the fence on the third-base side. During the last two weeks of the 2011 campaign, Andino had three clutch hits that helped prevent the Boston Red Sox from clinching the American League Wild Card. The first was a two-out bases-clearing double down the right-field line off Jonathan Papelbon in the eighth inning of a 7-5 win at Fenway Park on September 20. Six nights later, on September 26, he became the first Oriole to achieve an inside-the-park home run at Camden Yards with a three-run shot off Josh Beckett in the sixth inning of a 6-3 triumph. With runners on second and third and two outs, he sent the ball to deep straightaway center field where it initially landed in Jacoby Ellsbury's glove. It was jarred loose when Ellsbury collided with the fence. Andino was able to score standing up when the relay throw skipped past Red Sox catcherJarrod Saltalamacchia. The feat was witnessed by his father, Robert Sr., who was attending a professional game involving his son for the first time. Andino struck against Papelbon again with a two-out game-winning single to left field in the ninth inning of the regular-season-ending 4-3 victory at home on September 28. This walk-off hit ultimately resulted in the Red Sox losing a spot in the playoffs, as mere minutes later the Tampa Bay Rays won on a walk-off home run by Evan Longoria against the New York Yankees, to clinch the playoff spot the Red Sox previously held. His clutch performances were dubbed by the Boston sports media as "The Curse of the Andino", an obvious pun on the Curse of the Bambino. On September 7, 2012, Andino hit his career-high seventh home run of the season against New York Yankees pitcher Cody Eppley.
On July 31, 2013, he was traded to the Pittsburgh Pirates for a player to be named later or cash. He was assigned to the Triple-A Indianapolis Indians, where he finished the season. On January 7, 2014, the Pirates signed Andino to a minor league contract with an invitation to major leaguespring training. He did not make the team and spent the season with their AAA affiliate in Indianapolis, becoming a free agent at the season's end.
On December 28, 2015, Andino signed a minor league deal with the Miami Marlins. He had his contract selected by the Marlins on August 14, 2016. He appeared in 13 games for the Marlins, and amassed a.292 batting average.
Second stint with Baltimore
On February 6, 2017, Andino signed a minor league contract with the Baltimore Orioles. On May 31, Andino was suspended for 50 games for testing positive for Adderall. He elected free agency on November 6, 2017.
