Michele's account on the social media platform disappeared on Saturday.
The actress has yet to address the deletion, but in recent days, she has been tagged in a number of abusive messages urging her to comment on the disappearance of her former Glee co-star Naya Rivera.
Rivera, who starred on all six seasons of Glee, went missing Wednesday after renting a pontoon boat.
The actress went out to Lake Piru with her son, Josey, and her son was later found asleep on the boat.
Rivera's life vest was still on the vessel, but she has not been seen since. As a result, a search of the lake is being carried out.
Michele and Rivera were said to be in a feud on several occasions during their time on Glee, with Rivera writing about her time working with Michele in her 2016 memoir Sorry Not Sorry.