Arencibia was drafted 21st overall by the Toronto Blue Jays in the 2007 MLB draft. He was assigned to Toronto's Low A ball affiliate, the Auburn Doubledays of the New York–Penn League. Arencibia struggled during the early part of the season but hit well during the stretch and into the playoffs, helping the Doubledays win the NY-Penn League championship. He began the 2008 season with the Dunedin Blue Jays of the Florida State League. By the FSL all-star break, he led the league or was near the top in many offensive categories, finishing the first half of the season batting .315 with 13 homers, 22 doubles and 62 RBI. He was named as the starting catcher for the Western Division in the FSL All-Star Game.