The San Diego Padres selected Decker in the first round, with the 42nd overall selection, of the 2008 Major League Baseball Draft.
He began his professional career in 2008 with 49 games with the AZL Padres in the rookie-level Arizona League, where he had a batting average of .352 and had five home runs and 34 runs batted in (RBIs), and three games with the Eugene Emeralds of the Class A-Short Season Northwest League, where he went 2-for-10, giving him an overall batting average of .343 for the season.
He played the full 2009 season with the Fort Wayne TinCaps in the Class A Midwest League, putting up a .299 batting average and .956 on-base plus slugging percentage (OPS) in 104 games with 16 home runs and 64 RBIs.
He was ranked among Baseball America's Top 100 Prospects heading into 2010.

Promoted to the Lake Elsinore Storm in the Class A-Advanced California League in 2010, Decker hit .262 with an .874 OPS, hit 17 home runs, and drove in 58 runs, but he was limited to 79 games by injuries.
When he was placed with the San Antonio Missions in the Class AA Texas League in 2011, Decker's average fell to .236, but he hit 19 home runs, stole 15 bases, and scored 90 runs in 133 games, holding his OPS at .790.
The San Diego Padres added Decker to their 40-man roster over the 2011-2012 offseason, and he started the 2012 season with San Antonio.
 He suffered from plantar fasciitis early in the season and then tore his plantar tendon on May 31, 2012.
This limited him to only 47 games and a .184 batting average, three home runs, and nine RBIs with San Antonio.
Combined with a nine-game rehabilitation stint with the AZL Padres in which he batted .296, hit a home run, and drove in seven runs, he played in only 56 games and had only a .201 average for the 2012 season as a whole.

Decker began 2013 with the Tucson Padres in the Class AAA Pacific Coast League.
The San Diego Padres selected Decker in the first round, with the 42nd overall selection, of the 2008 Major League Baseball Draft. He began his professional career in 2008 with 49 games with the AZL Padres in the rookie-level Arizona League, where he had a batting average of .352 and had five home runs and 34 runs batted in (RBIs), and three games with the Eugene Emeralds of the Class A-Short Season Northwest League, where he went 2-for-10, giving him an overall batting average of .343 for the season. He played the full 2009 season with the Fort Wayne TinCaps in the Class A Midwest League, putting up a .299 batting average and .956 on-base plus slugging percentage (OPS) in 104 games with 16 home runs and 64 RBIs. He was ranked among Baseball America's Top 100 Prospects heading into 2010.
Promoted to the Lake Elsinore Storm in the Class A-Advanced California League in 2010, Decker hit .262 with an .874 OPS, hit 17 home runs, and drove in 58 runs, but he was limited to 79 games by injuries. When he was placed with the San Antonio Missions in the Class AA Texas League in 2011, Decker's average fell to .236, but he hit 19 home runs, stole 15 bases, and scored 90 runs in 133 games, holding his OPS at .790. The San Diego Padres added Decker to their 40-man roster over the 2011-2012 offseason, and he started the 2012 season with San Antonio.  He suffered from plantar fasciitis early in the season and then tore his plantar tendon on May 31, 2012. This limited him to only 47 games and a .184 batting average, three home runs, and nine RBIs with San Antonio. Combined with a nine-game rehabilitation stint with the AZL Padres in which he batted .296, hit a home run, and drove in seven runs, he played in only 56 games and had only a .201 average for the 2012 season as a whole.
Decker began 2013 with the Tucson Padres in the Class AAA Pacific Coast League.
Jaff Decker