49ers: Why was Kyle Shanahan extended and not John Lynch?

The San Francisco 49ers extended Kyle Shanahan, but why haven’t they done the same for John Lynch?

The San Francisco 49ers made the decision to extend head coach Kyle Shanahan on Monday to the tune of a massive six-year deal replacing the final three years remaining on his contract.

The move was understandably praised by both fans and the national media alike with most claiming the decision to extend him to be a sound one. However, it left many asking one question, in particular.

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What about general manager John Lynch?

Lynch and Shanahan have been tied at the hip ever since their arrival in San Francisco back in 2017. The duo has overseen a complete overhaul of the organization and is the leading force behind the team’s newfound success.

So then, what gives? Why extend Shanahan but leave Lynch hanging? NBC Sports’ Matt Maiocco seemed to insist the reasoning in a recent interview with KNBR’s Murph & Mac on Wednesday morning.

Maiocco spoke about how this was definitely the right time to extend Shanahan despite the fact that he had three years remaining on his contract. The main reason for this? His poor compensation.

While coaches’ contracts are rarely made public, Maiocco insisted that Shanahan probably wasn’t being fairly compensated. He specifically cited Cincinnati Bengals head coach Zac Taylor who “reset the market” when he was hired last offseason.

There’s really no reason that Shanahan should have been making less money than Taylor so the 49ers sought to right that wrong. Maiocco gave a pretty clear indication of where Shanahan stands amongst other coaches now.

"“The 49ers made it so Kyle Shanahan, depending on what metric you use, you can work the numbers to make him the third highest paid coach, or as low as the sixth. So he kind of falls into that area. When you look at it that’s about right, that’s about where he should be.”"

As Maiocco said, that is probably exactly where Shanahan should be. The timing of his extension makes sense, even if the 49ers would have rather not announced it in the middle of a pandemic.

For Lynch, however, things are a little different.

Why have the 49ers not extended John Lynch as well?

Maiocco pointed out that Lynch is already among the highest-paid general managers in the NFL. The 49ers had to convince Lynch to leave a “pretty lucrative” job calling NFL games for FOX so they undoubtedly paid him well.

And for that reason, there isn’t as much of a hurry to extend Lynch. Maiocco also noted that the general manager market could be reset in the coming years.

"“And I don’t think you can give John Lynch a salary bump when he hasn’t won a Super Bowl, but there are some general managers that are coming up on their contract — guys like Mickey Loomis (Saints) and John Schneider (Seahawks) — and I think once the market resets, if the 49ers continue the path they’re going on, John Lynch will get a contract that resets his market and ties Lynch and Shanahan together through that 2025 season.”"

That quote pretty much says it all. The 49ers fully to keep both Shanahan and Lynch together for the long haul (why wouldn’t they?). But the timing made more sense for their head coach than their general manager.

Simply put, Lynch is already being fairly compensated and the market hasn’t been reset yet. Shanahan, on the other hand, was not being fairly compensated and the market had already been rest by the Bengals.

Next. 49ers: Why the team should consider a reunion with Colin Kaepernick. dark

And that, in the simplest terms possible, is why Shanahan was extended and Lynch was not.