Murphy announced that the show, which follows the trials and tribulations of a high school show choir, will air two previously written episodes that pay tribute to the Beatles as well as an episode that addresses the death of Monteith's character, Finn Hudson.
Following those three episodes (the premiere is delayed until Sept. 26), the show will take a long hiatus.
As previously reported, Monteith died July 13 from an overdose of heroin and alcohol.
The decision to resume shooting was a collective decision made by the cast and crew, including Michele, Murphy said, who decided the best way to mourn Monteith's death was to return to work and mourn together. Grief counselors will be on set for two weeks. Monteith had spoken openly about his struggles with drug and alcohol addiction, and Murphy participated in an on-set intervention that resulted in Monteith checking into rehab for substance abuse in March 2013.
"It is so very sad and tragic," Murphy said to Deadline. "Cory wasn't just an actor on one of my shows, he was very important to me, and I was very invested in his sobriety. When I heard what was happening to him, I organized an intervention and got him into rehab last March. We socialized and we also fought, because while he was a lovely sweet guy, he was also a leader on the set, a strong personality and the only analogy I can think of is that he felt like an older son to me."
Many fans responded to the announcement that "Glee" would resume shooting by saying it was insensitive and too soon to return to work, but Murphy said the cast and crew support the decision.
"For many of the people we work with who are very young, and also for the fans of the show, this is probably the first time they have experienced death, and that was not lost on any of us here," Murphy said to Deadline. "I understand that everyone has their own way of processing grief. Every possible option was explored, and what we did was look to the people who loved Cory, who worked with him most, and specifically Lea. This is what they wanted to do."
He said he hopes the death of Monteith, and addressing it on the show, will help others in the future.
"One of the most gratifying things about 'Glee' is that when the show is at its best, it has helped young people and given them information about the human condition that moves and informs them," Murphy said. "What we've been talking about in the writer's room is that maybe the way we deal with this tragedy might save the life of someone."