Ben Cherington didn’t just defend the Pittsburgh Pirates’ decision to limit Jared Jones to five innings at the New York Mets on Tuesday but also applauded the coaching staff for coming up with the plan.

The 22-year-old rookie right-hander was pulled despite holding the Mets scoreless and to one hit without a walk while striking out seven in an extremely efficient start that saw him throw strikes on 50 of 59 pitches.

Cherington noted it was the first time Jones had pitched on four days of rest in the major leagues. The Pirates ended up losing the game 3-1 on their way to getting swept in the three-game series.

“The staff decided on their own that we’re going to hold him a little bit short this time,” Cherington said Sunday afternoon on his weekly radio show on 93.7 FM. “It’s a long season and we want Jared Jones to be part of this for the long season. I really respect their decision. It’s not easy to do that in the middle of a game you’ve got a chance to win with a guy pitching as well as he was. I really respect that decision, to have some perspective that this is a long war we’re fighting in 2024 and there’s these individual daily battles we’re trying to win. We’re trying to make decisions to do both, win the small battles and win the war.”

The Pirates have drawn criticism for having both Jones and top pitching prospect Paul Skenes, the No. 1 overall pick of the 2023 MLB Draft, on a short leash early this season despite dominant performances.

Skenes hasn’t allowed a run in 12 2/3 innings over four starts, recording 27 strikeouts against five hits and four walks. But he hasn’t thrown more than 65 pitches or gone past 3 1/3 innings in any of those starts.

“He’s going to get there. We just chose to do it a little bit more slowly coming out of spring training,” Cherington said. “We want him to be in a position to compete for a full season. Given his abilities and what he’s doing, we also want to leave open the possibility that that’s at the major-league level. We’re just trying to put him in the best position to do that.”

Cherington said he received multiple inquiries last week about the Pirates’ innings and pitch count restrictions on their young starters, with a common question: How do you know you’re right?

“The answer is, I don’t. We don’t know we’re right,” Cherington said. “We can’t be certain that we’re right about these decisions and how we are going about it. What we’re working to do and trying to do every day is to be as thoughtful as we can, based on all the inputs we have and all the information we have — and there’s a lot of it. A lot of it comes from the pitcher himself, some of it comes from other sources, from history and research. Factoring all those inputs, including the team winning games — that’s the most important input — and make the best decision we can that put a pitcher in position to help the Pirates over time win the most possible games. That’s the goal.”

Cherington also addressed several players dealing with injuries, most notably the catchers. Jason Delay underwent surgery on his right knee, but Cherington called it “the best-case scenario we could have hoped for” because he was walking around and feeling better two days later.

Veteran Yasmani Grandal, who missed most of spring training with plantar fasciitis in his left foot, is on a rehabilitation assignment with Triple-A Indianapolis. Cherington said the Pirates figure that Grandal “isn’t too far” from being activated to the major-league roster.

Switch-hitting catcher Endy Rodriguez, recovering from Tommy John surgery on his right elbow, will begin a formal hitting progression from the left side around May 1. Cherington said Rodriguez will begin throwing before he takes swings from the right side, but the Pirates aren’t planning on him playing this season, even in a designated hitter role.

“We haven’t made any total firm decisions, but it’s not something we’re expecting right now,” Cherington said. “If we get further in the calendar, it’s something we could revisit.”

Cherington also credited left-hander Marco Gonzales, who is on the 15-day injured list with a left forearm muscle strain, with recognizing that something wasn’t feeling right even though he didn’t show any outward signs of injury.

“He was out there. His velo was holding. He was still executing pitches,” Cherington said. “He was feeling something … and surprised himself that it wasn’t getting in the way of execution. … What he has is something, hopefully, we caught relatively early and is relatively minor.”

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