MINNEAPOLIS — When Jim Pohlad came to what he called “a stomach-churning” conclusion that general manager Bill Smith needed to be fired, the Minnesota Twins owner was making the kind of decision rarely seen in one of the most loyal and patient organizations in baseball.

A 99-loss season is equally unique in these parts, so Pohlad swallowed hard, made the move and turned to one of the most trusted and revered figures in the organization to pick up the pieces.

Terry Ryan reclaimed the job he had for 13 years on Monday, taking over for the man he recommended to take his place when Ryan stepped down four years ago.

“In the past week, it was clear to all of us that a change in leadership was in the best interest of our organization,” Twins President Dave St. Peter said. “We proceed with that change with a high level of respect and sensitivity to Bill Smith and his family.”

Widely recognized for their stability, class and ability to make the most out of a medium-range payroll, this was a startling move for the Twins despite the embarrassment and deep disappointment of the 2011 season following two straight AL Central titles.

This is the first time since the franchise moved from Washington to Minnesota in 1961 that the Twins have fired a general manager. Calvin Griffith was the owner and general manager until selling the team in 1984. Andy MacPhail became the full-time successor, leaving for a prime job with the Chicago Cubs, and Ryan followed him. They’ve also had two managers — Tom Kelly and Ron Gardenhire — since 1984.

“We do this with a heavy heart,” Pohlad said. “But we also do this knowing that it is what’s best for the organization.”

Pohlad and St. Peter both side-stepped numerous questions about the specific reasons for the decision, saying it came down to “philosophical differences” in the direction of the baseball operations.

Ryan remained in the organization on the scouting level and said he turned down several inquiries from other teams about taking over a front office again. On Monday, he said his “batteries are recharged” and he’s ready to get back to work.

“I’m going to take this job head-on,” Ryan said.

It appears to be an interim job in name only. Ryan said he would have a role in grooming and choosing his eventual successor, but both he and Pohlad said they hoped things went well enough where Ryan would want to keep the job for a while.

“I don’t know if it will be for one year or 10 years,” Ryan said. “(I’m) going to see how it goes and see exactly the direction and success and workload and all the things that about 4 1/2 years ago we talked about over at the Dome.”

Ryan’s moves helped turn the Twins from one of the worst teams in baseball in the mid-90s to one of the best the next decade. They won four division titles over Ryan’s last five full seasons, without spending much money in free agency and instead drafting and developing their core players.

Shrewd trades were part of his success, too, fetching Cristian Guzman and Eric Milton for Chuck Knoblauch; getting Nick Punto and Carlos Silva for Milton; and landing Francisco Liriano and Joe Nathan for A.J. Pierzynski.

Smith’s decisions haven’t turned out as well, dealing Johan Santana, Matt Garza, J.J. Hardy and Delmon Young for little production in return. Japanese shortstop Tsuyoshi Nishioka, the headliner acquisition last winter, was hurt for much of the season and a bust at the plate and in the field.

Pohlad added that the Twins will speak with Smith about “an ongoing role within the organization.” Smith has been with the club since 1986.

“This is going to be good for the Minnesota Twins organization,” Smith said in a phone interview. “It’s always tough when it involves you, but at the same time I respect the decision that the Pohlads had to make. We have to do it with players all the time, and it’s no fun.”

The Twins were division champions under his watch in 2009 and 2010, but this season was a mess.

Injuries to Jason Kubel, Joe Mauer, Justin Morneau, Nishioka and other key players didn’t help, but the most expensive team in Twins history — with an opening-day payroll of more than $112 million — prompted Pohlad and the rest of the front office to take a hard look at an organization that has frequently been lauded as one of the finest in the game. The top of the farm system has dried up in recent years, and the rebuilding project will be a challenge for Ryan and the rest of his support staff.

Smith acknowledged when he was hired his strengths lied in administration and operations. He didn’t play the game or scout it like Ryan did. He worked heavily with the team’s development academies in Venezuela and the Dominican Republic, and he played a large role in the plans to design Target Field, which opened in 2010.

“I love the Twins organization. I’ve been very fortunate that for 26 years, every morning I get up I can’t wait to get to work,” Smith said. “There aren’t very many people who can say that.”

The 58-year-old Ryan said he planned to bring former Twins executive and Reds GM Wayne Krivsky on as a special assistant and said the team’s payroll likely would be trimmed to around $100 million next season.

One of his priorities will be to address the medical side of the team. Several injured Twins spent an inordinate amount of time on the disabled list, and Ryan said the team has to figure out why they didn’t get back sooner.

“We need to do some tweaking at the very least there. … I know Bill was in the process of doing that up until last week,” Ryan said. “He was worried about it and I’m worried about it. … The players can only take advice. Players take the advice you give them. … I would never put it on the players. It’s our responsibility to take control of that and we will.”