Almonte got the start in left field on Wednesday in the series finale against the Giants at Petco Park.
Middlebrooks was hitting .212 with nine home runs and 29 RBIs in 83 games this season. Since June 6, he hit .133 and had lost his starting job to Yangervis Solarte. The Padres have given him three starts at shortstop since July 11, but he'll play more third base in El Paso.
"Will is a very talented guy, and he needs to go down there and find himself ... get consistent at-bats, not in and out of the lineup," said Padres interim manager Pat Murphy. "Play third, play short and come into his own. It might take a week, it might take two weeks, a month. It might take two months.
"We want to see if we can light something in Will. We've got to do something. ... That guy is a valuable piece."
The decision to option Middlebrooks means Solarte will get the most of the starts at third base moving forward, with Clint Barmes seeing the majority of time at shortstop and Alexi Amarista staying in a utility role.
Murphy hopes that Middlebrooks can find success in Triple-A and get back to the big leagues.
"Ultimately we would like him to come back as the starting third baseman. We hope he finds himself down there, get some good at-bats. This has been a trend in his career the last couple years," Murphy said. "It is very common for a lot of players to go through this, but it's time for him to go out there and work it out."
Almonte was hitting .275/.361/.414 in 61 games with El Paso with 24 extra-base hits, 35 RBIs and 11 stolen bases. He can play all three outfield positions and offers a speed component.
Almonte gives the Padres a little extra outfield coverage with Justin Upton still working his way back from a tight left oblique. Upton missed his third consecutive start on Wednesday, though the team believes he'll return by the weekend.
In Almonte, Murphy has a player he is familiar with, as he was his manager in El Paso before being named interim manager of the Padres last month.
"He knows who he is in the game," Murphy said. "He has an identity. That identity enables him to run, to bunt, hit and run, get behind runners, contact, and he's got a little juice in him, too. Hopefully he can ignite us a little bit."
Corey Brock is a reporter for MLB.com. Keep track of @FollowThePadres on Twitter and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.