Dave Dombrowski used the first eight months of his time with the Phillies to observe the organization, leading to a discovery that caused him Tuesday to remove the director of player development along with two assistant general managers.

Josh Bonifay, the team’s farm director since October 2018, was offered a position for next season as a pro scout while assistant general manager Bryan Minnitti, who oversees player development along with amateur and international scouting, will be a consultant in 2022. Scott Proefrock, an assistant GM since November 2008 who handles league rules and assists with contract negotiations and salary arbitration, will also be a consultant next season.

It was the first significant change to the front office since Dombrowski became the Phillies’ president of baseball operations in December.

Bonifay and Minnitti were both hired by former general manager Matt Klentak and are largely responsible for a farm system that was ranked earlier this month by Baseball America as the third-worst in baseball. The Phillies spent five seasons with a top-10 draft pick yet will often field a lineup during a playoff chase with just one homegrown player.

The team’s failure to reach the playoffs cost Klentak his job after last season. On Tuesday, the lack of production from the minor leagues spelled the end for Bonifay and Minnitti.

“You get to this time of year and you’re generally talking about the 2022 season and before you’re ready to do that, you have to make sure the people who are running things for you are the people who are going to correct it,” Dombrowski said. “I just thought it was appropriate to make some changes.”

Dombrowski said he does not know who will replace Bonifay, but the new leader is expected to have a more balanced approach after the farm system has aggressively implemented new methods in recent seasons.

“I believe in a balance of traditional methods with bringing as much contemporary information as you possibly can,” Dombrowski said. “It’s a big job. It’s a hard job. It’s not easy. To me, if I say, OK, 30 years ago, well, we did this. And we did, but we’ve learned a lot more since then. So, you look back, well, how do you incorporate both of them together? It’s hard. Really smart people that I know struggled with doing both of them. So we need to make sure it comes from me on down that this is what we believe, contemporary and yet traditional.”

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Under Bonifay, the Phillies heavily embraced new-age teaching practices and methodologies while pushing out a cast of veteran coaches and staff members whose tenure with the organization predated Klentak’s regime.

The Phillies targeted coaches who were tied to Driveline, a baseball laboratory in suburban Seattle that studies biomechanics and uses cutting-edge technology to train players. Their current hitting coordinator, Jason Ochart, remains on staff at Driveline while Travis Hergert, who replaced longtime minor-league pitching coordinator Rafael Chaves in March, utilized Driveline methods during his time coaching at an Iowa junior college.

The new direction provided mixed results. In three seasons under Bonifay, the farm system has produced just one position player who has been worth more than 0.5 Wins Above Replacement. Just one hitter on the current roster — reserve Luke Williams — was in the Phillies’ minor-league system during Bonifay’s tenure.

The Phillies have used 24 starting pitchers since 2019, and just one player who reached the majors since 2019 has started more than three games. The current staff includes three pitchers — relievers Connor Brogdon, J.D. Hammer, and Bailey Falter — who reached the majors while Bonifay was overseeing the minors.

“I don’t think we have enough people on the same page,” Dombrowski said. “I don’t even want to say swinging one way or the other. I think it’s going to be imperative that if we’re going to be as good as we can be that you buy into the way we do it or not be here. And I think honesty is extremely important. It’s different if you disagree and we talk about it and you say, ‘OK, I’m good. I got my piece in’ and we move forward. But if you can’t do that ...”

The Phillies will spend the next six weeks vying for their first postseason berth in a decade. But they’ll lean mostly on players who were signed as free agents or acquired before Klentak’s regime was in place. The seasons of losses were meant to produce the type of home-grown core that the Phillies rode to their last world championship. But that production failed to come. And Dombrowski believes his observations gave him an idea of how the Phillies have fallen short.

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“I think the people themselves, I like the individuals,” Dombrowski said. “I think they’re really sharp individuals but myself personally, I think some of them may be a miscast situation.

“We have to take a position to properly develop them, to work with them. So it’s a huge job for anybody. That’s why for me, I also like working with Sam Fuld because he brings some other thought processes to an evaluation, which I think are very good. It’s a big job. It’s a big responsibility, but I think we’ll get it right. But we have to make sure that this hire is a good hire for us.”