Just over a week after turning down the opportunity to manage Huddersfield, he will be sat in the dugout at the John Smith's Stadium on Sunday as his new side takes on Sheffield Wednesday, live on Sky Sports Football.
But what changed for him?
"I think the major change for us was the opportunity to manage the club," he told Sky Sports. "We see this as a long-term project, probably three years. The success we have had at previous clubs is when we could manage, or at least have an involvement, in every area of the club.
"As a head coach you look after the team on the grass and on the pitch, but that isn't enough for me. I like to win on a Saturday but also have the opportunity to build a club, that is what me and Nicky have done before and that is what gives us our satisfaction.
"That was hugely important for us and now we feel we can have an impact on the academy, which is important for sustainable success here. We can also impact the medical and sports science work that is going on here, and also the recruitment side of things. That is such an important part of being successful.
"We have to be realistic of where we are now. We are in a relegation battle. What we have got to try and do is consolidate our status in this division and then build towards being more competitive next year, maybe finishing top 10. Then hopefully we will have some foundations by that stage to go from there and achieve another football miracle."
Cowley, along with his brother and assistant Nicky, have taken the leap from Lincoln - who are near the top of League One - to Huddersfield, currently with just one league win in 2019 and occupying 23rd spot in the Championship.
Cowley could have heeded recent lessons from lower-league managers who have struggled when making the step up to the Championship. Paul Hurst and Nathan Jones are two who have recently laboured after leaving upwardly-mobile League One clubs, but the 40-year-old believes he has what it takes to turn the situation around at Huddersfield. But it won't be a quick fix.
"It is a mentality thing," he said. "We have spoken to a lot of people around the club who think they are one win from changing that, but I'm not so sure.
"To impact people's confidence and give people belief it's about the process and methodology of how you work. It's about giving the group a clear gameplan and the players clarity of their roles and responsibility within that, and then it's about rehearsing and understanding the performance.
"When you develop that you get a bit of alignment, and then the players start to rehearse that and get some successes, and then they build confidence. It is a gradual process and it does take time. We have made some good gains so far in the days we have been in, but there is a long way to go.
"I think the aim is to try and bring some values that are important to us and try to reflect those within the football club. There are some non-negotiables for us in terms of our relentless work ethic, discipline and respect, but also enthusiasm and humility.
"You've got to enjoy what you do and when you do well you've got to stay ground and focused, and keep wanting to learn and move forward. They are the values we try to live to every day and what we try to instil. That certainly allowed us to get success to this point and for us that gives you the foundation to bring our processes through.
"I wish I had a magic wand but I don't. What I do have is a huge amount of enthusiasm and a relentless work ethic. And I'm lucky to have Nicky with me, who has that as well."
The opportunity for himself and his brother Nicky to take over a club that were in the Premier League just a few months ago must have been difficult to refuse, particularly when you consider where they have come from, but the ties they had forged at the club made his departure incredibly difficult. Only an opportunity that was impossible to turn down would have lured him away.
"It was the toughest decision of our lives because of the relationships we had built there and the loyalty we felt to the people and the club," he said. "They were brilliant with us and we had a wonderful relationship with the supporters.
"We were also completely aligned with the board of directors and had a really hard-working group of staff that all started with us at the beginning , mostly as interns and volunteers, and we built it up with them. We had a really talented and hardworking group of players, and it was really hard to leave.
"It did feel a bit like a mourning process, I know that sounds dramatic! But it was emotional. We lived every moment of that journey and we will forever be proud of what we achieved there. We believe we left the club in a really good place and we know they will continue to have success.
"But Nicky and I are very impatient and we want it now. It's not Lincoln's moment to be really aggressive because they need to establish themselves in League One first, and we were offered the opportunity to manage a brilliant club like Huddersfield.
"It is a daunting job due to their incredible history, and with some of the managers who have been here, but that is what life is. I want to wake up in the morning with the excitement of being challenged, I want to feel the heat. That is what living is to me."
From Concorde Rangers in the Essex Senior Football League to Huddersfield in the Championship. Cowley has been through nearly every division in senior football - except for the one right at the top.
He and Nicky, however, have early roots in management that may seem far more familiar to the average football fan.
"People say it started with Championship Manager, and we did play that a lot as children, we would often start with a lower-league team and work through the divisions," he said. "Mum would tell Nicky to stop playing it and get on with his homework, and Nicky now tells her that if she had allowed him to play it a little bit longer than maybe we would be in the Premier League right now!
"But it has been an incredible journey for us and the fact our family has been part of it all the way makes it an even prouder moment for us. I wouldn't change my pathway for the world, I learned so much from teaching and to start at the bottom of non-League and develop my skill-set from there has been a wonderful journey. I have learned lots along the way and I am looking forward to learning a lot more.
"We didn't come this far to only come this far. We have now managed in nine of the top 10 divisions, that is something we are really proud of but obviously we would like to manage in the 10th one."