After spending his first year learning how to run an NFL organization while observing the staff he led, John Elway is taking charge.

In year two, Elway has made a series of significant changes as he continues to reshape the Broncos to meet his vision.

When it became apparent Monday that Elway’s vision and general manager Brian Xanders” career desires would never quite intersect, the two front-office executives mutually decided to part ways. Xanders, who had been with the Broncos four years, the last three as a general manager, leaves with one year left on his contract.

“John and I had a lengthy conversation today and we mutually decided to part ways for the best interest of my career aspirations,”” Xanders said. “I appreciated everything that (owner) Pat Bowlen has done for the Broncos and for bringing me here in 2008. It was great working with Coach John Fox. I’m telling you, he’s a great coach to work with, and it was great working with John Elway.”

” Xanders had worked 14 years in a variety of capacities with the Atlanta Falcons before he was hired to become the Broncos” assistant general manager by then-coach-football operations boss Mike Shanahan after the draft of 2008.

Xanders, 41, was promoted to general manager the next year by then-coach-football operations boss Josh McDaniels, a position Xanders held until Monday.

General manager had long been Xanders’ dream position, but his first big gig never came with the final-say authority on roster personnel. Shanahan had final say in 2008, McDaniels had the power in 2009-10 and then Elway was hired to take control of the front office in 2011-12.

“No question, I think everybody would like to have that position with that type of control, especially a general manager,”” Elway said. “That was something we discussed. Hopefully, someday Brian will be in that position where he is making all the decisions in the end. That is a desire of his. He knows a lot of people in this league and is well-respected in the league.”

In Elway’s first year as the Broncos’ vice president of football operations in 2011, Xanders helped guide him through the administrative procedures and policies that come with the top NFL front-office job.

Meanwhile, Elway observed his own staff for a year without making any major changes, as McDaniels did when he first took control in 2009.

But to begin his second season as the man in charge, Elway has made some strong, boss-like decisions. No move was more substantial than at quarterback, where Elway lured free-agent Peyton Manning and traded away Tim Tebow.

Elway’s biggest off-field moves seemingly have been made to streamline the Broncos” football operations. He promoted Matt Russell from director of college scouting to director of player personnel, which means he oversees talent both on the NFL and college level. Elway also hired former agent Mike Sullivan to become the team’s new man in charge of contract negotiations and the salary cap.

“It is a streamline; we’re not adding anybody,”” Elway said. “Brian has a great heart and is a loyal guy. He’s the type of guy who would give you the shoe off his foot. This is the worst part of this business.”

Although the Broncos’ 2009 draft bombed, the McDaniels-Xanders’ regime had only 3½ months to prepare. The Broncos” drafts in 2010 and 2011 were among the league’s best. Starters produced from the 2010 draft were Demaryius Thomas, Tebow, Zane Beadles, Eric Decker, J.D. Walton and Perrish Cox. In 2011, Von Miller became the NFL defensive rookie of the year and Orlando Franklin was a 16-game starter. Safeties Rahim Moore and Quinton Carter were also starters.

Those 2010-2011 drafts produced the most starts (155) and playing time (more than 12,000 snaps).

“As I look back, it was an accomplishment that we were able to draft so many of those guys and get them on the field and playing right away,”‘ Xanders said.

Elway was also happy about the players the Broncos recently drafted, a class headed by defensive tackle Derek Wolfe, quarterback Brock Osweiler and running back Ronnie Hillman.

With the draft concluded, Elway has re-shaped the front office so Russell and pro personnel director Keith Kidd are now directly below him on the football operations organizational chart.

“It was tough because I have a great deal of respect for Brian as a football man but also as a person,”‘Elway said. “Even more so as a person. He was very helpful to me in this first year getting acclimated back to the NFL. I owe him a lot. Just from the conversation we had, we just thought for his career and for the Broncos we felt that now was the best time to go a different way.””

Mike Klis: 303-954-1055 or mklis@denverpost.com