The 40-year-old has decided to return to his position as Academy manager after spending the last six months helping out Guy Whittingham with the first team.
Awford felt his talents were more suited to developing youngsters rather than helping coach the senior players.
"It was a really tough decision, but a lot of hard work has gone into the Academy over the last two-and-a-half years and that's not something I want to give up," he told the club's official website.
"I'm really proud of what we've achieved and I want to see the job through. The Academy staff deserve enormous credit for their fantastic work over the past couple of seasons.
"I've loved working with the first team and it was a big learning curve for me to deal with seasoned professionals.
"It was an exciting venture and one I enjoyed thoroughly, especially towards the end of the season when we were more settled.
"But now there's an opportunity to rebuild this football club and I feel proud and privileged to be a part of that."
Pompey boss Whittingham added: "I totally understand and respect his decision. He has put a lot of effort into the Academy here.
"It's important for this football club that Andy and all of the Academy staff know what is needed to produce players for the first team."