The actress explained that the Glee team want to experiment with putting distance between Rachel and Monteith's character Finn following their break-up in May's finale.
Speaking at this year's Comic-Con, Michele told E!: "I definitely think they saw us together a lot, so I think they want to sort of see what it's like for them to sort of be apart for a little while now.
"I think that's the dynamic, that's the dance where they pull them apart and being them back together.
"I love working with Cory so I'm sad we won't get to work together too much, but they'll always be involved with one another whether or not they are dating."
Michele and Monteith previously revealed that they are both preparing for physically demanding storylines in Glee's fourth season.
Michele has also revealed one of the songs she will be covering in the premiere.
Glee returns to Fox on September 13.