Mpanzu penned a new deal that runs until 2020, with the potential for a further year.
He became the second Town talent this week to commit his long-term to the club, as defender James Justin extended his deal for the same period on Monday.
Jones said of Pelly: "He's not quite a youngster anymore, but he's developing. We are pleased we have secured him for another three years and he's one that has attracted a little bit of attention, so it's pleasing that they trust us with his development.
"We've tried to tie everyone down once we know we want to move forward with them. We're not backward in coming forward in terms of tying them down. We have all the players in terms of the ones we want. We have a real nucleus of players under long term contracts and it's something to build on.
"What we are looking at short term is them doing well for Luton Town and developing all aspects of their career. Whatever happens in the future – hopefully they move forward with Luton Town and Luton Town move forward very, very quickly – they keep pace with our development and we keep pace with their development.
"If anything happens differently, then we will have a decision to make. We're delighted though. We have got a settled squad now and we are looking forward to the season."
The former Brighton & Hove Albion assistant-manager also hopes to see Pelly improve a certain side of his game, as he already has the attributes to go onto be a top quality central midfielder.
"There's certain things that we have requested from him – his final third play needs to improve a little bit because everywhere else he's potent," Jones explained. "He works hard, he covers big distances, he keeps possession for us, he's very brave and it's just that final third we are asking him to add a little bit more quality. That'll come in time I am sure and if it does then we have a real player on our hands."
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