The forthcoming ABC drama focuses on an elite spy organisation and will star Clark Gregg as Agent Coulson, alongside Ming-Na, Elizabeth Henstridge, Iain De Caestecker and Brett Dalton.
Whedon told Entertainment Weekly that working on a sequel to The Avengers is his "number one priority" but added that he will be involved with S.H.I.E.L.D. as his "schedule allows".
"I have to maintain a fine balance between not hurting The Avengers... and [also] not be the guy who shows up once a month and undoes everything that's been done by everyone else," he explained.
Whedon's brother Jed will work alongside Melissa Tancharoen and Jeffrey Bell on the day-to-day production of S.H.I.E.LD. with Whedon himself serving as executive producer and also direct the show's pilot episode.
"One of the great things about having worked for so damn long is that there are so many people that I truly trust," he said.
Pacific Rim director Guillermo del Toro recently claimed that his own Marvel TV series - a show featuring the Hulk - has been put on hold by ABC.
> Samuel L Jackson wants role in Joss Whedon's S.H.I.E.LD. pilot
> Joss Whedon's S.H.I.E.L.D. pilot "very exciting", says ABC boss
Watch a clip from The Avengers below: