Ellis went 1-1 with a 4.50 ERA across three games with the Portland Beavers. In 4.0 innings he allowed four hits, two walks and struck out one. He allowed one homer while holding the opposition to a .250 average.

Ellis went 9-6 with a 3.19 ERA across 57 games with the San Antonio Missions. In 73.1 innings he allowed 73 hits, 31 walks and struck out 70. He allowed three homers and induced seven double play grounders while holding the opposition to a .260 average.

2007

He was invited to play in the Arizona Fall League after the year.

Ellis went 1-0 with a 2.70 ERA over four Missions playoff games. In 3.1 innings he allowed three hits, a walk, and three strikeouts.

2006

Jonathan Ellis was suspended 50 games during the 2006 season for violating the Minor League Drug Treatment and Prevention Program.

Ellis went 0-1 with a 2.30 ERA over 12 games, including two starts, for the Mobile BayBears. In 15.2 innings he allowed 20 hits, walked six and struck out 17. The opposition hit .317 off him.

Ellis went 1-2 with one save and a 2.57 ERA in 24 appearances for the Lake Elsinore Storm in 2006 before being promoted to Double-A.

Ellis pitched in one game for the AZL Padres, allowing an unearned run on a walk in an inning of work.

2005

Ellis went 5-3 with a 3.89 ERA in 43 games for the Fort Wayne Wizards, including five starts. In 78.2 innings he allowed 82 hits and 24 walks while striking out 69.

2004

Ellis pitched in just five games before an injury claimed the rest of his season. He had a 4.66 ERA and had a seven inning scoreless streak to end the year.

Notes

The junior from The Citadel was picked in the sixth round by the Padres after setting single-season school records with 136 1/3 innings pitched and nine complete games. Was 12-3 this year with a 2.18 ERA and was named to the all-Southern Conference team and the all-tournament team at the Columbia Regional. Was named most valuable player of the SoCon Tournament after pitching two complete games.