Samardzija was optioned to the Minor Leagues on Saturday to make room on the Cubs' roster for Ted Lilly, who was activated from the disabled list and made his first start Saturday night against the Milwaukee Brewers.
Samardzija will stay in the bullpen for Iowa rather than start, as he did last season.
"We've got a lot of starting pitching here," said Cubs manager Lou Piniella. "For him to get back quicker, out of the bullpen would be the easiest way."
With the Cubs' decision to move Opening Day starter Carlos Zambrano to the bullpen, the team had too many right-handers. Samardzija compiled an 18.90 ERA in four relief appearances, having given up seven earned runs on five hits and six walks over 3 1/3 innings.
"We've done it before, sending him down [to the Minors] and starting him and bringing him back up as a reliever, and that hasn't worked too well," said Cubs pitching coach Larry Rothschild. "He's going to go down there and relieve, and as he gets situated in relieving, hopefully be in close games and get ready to be in the bullpen."
Among the other right-handed candidates, Jeff Gray has given up three earned runs on six hits and two walks over five innings, for a 5.40 ERA, and Justin Berg has given up four earned runs on six hits and three walks over seven innings, for a 5.14 ERA.
In his previous outing, on Monday in New York, the 25-year-old Samardzija did not record an out, giving up a hit and walking one. He had served up runs in three of his past four appearances.
"He's got good stuff," Piniella said. "His command needs to improve, that's probably the biggest thing for him. Going down there, pitching out of the bullpen in late innings, will get him better prepared."
Samardzija began this season as a candidate for a spot in the Cubs' rotation, and has made it clear he'd prefer to start. This spring, Piniella said he felt Samardzija had made progress, and, for the first time, looked more like a pitcher than a football player trying to pitch. Samardzija starred at Notre Dame as a wide receiver.
"Often when you put a guy starting in the bullpen, you see the guy transition and have more power and go after guys aggressively, and that didn't happen in this case," Rothschild said. "I think he was still trying to keep himself under control a lot. I think it's getting adapted to what you have to do and prepare as a reliever."
Samardzija was 6-6 with a 4.35 ERA in 18 games (17 starts) with Iowa last season, and 1-3 with a 7.53 ERA in 20 games (two starts) with the Cubs.
"To his detriment, we've moved him where we've needed him back and forth, and that's not the easiest thing to do," Piniella said. "You try to use players' talents where they're needed, and sometimes for the player, it's a little more difficult transition."
The move doesn't mean Samardzija will never start again.
"Right now, our needs are in the bullpen, and I think he's best suited for that," Rothschild said. "We could do the same thing and send him down as a starter, but it hasn't been the right thing in the past. It wasn't wrong, but it didn't work right."
Carrie Muskat is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.