The Mesolithic era at Theopetra dates between 9700 and 6500 BC (9700-7800 BP). In the upper layers of the Mesolithic, an intact (in situ) burial in contracted position was unearthed dating to 7050-7010 BC; it resembles burial practises such as those observed at Cave Cyclops in Yioura, at Franchthi Cave in Hermionid, and at the open Mesolithic site Maroulas on Kythnos.

The diet of the Mesolithic settlers included wild barley, wild lentil and lithospermum. Among the animal bones bones of wildgoats, cattle, some carnivores, birds, mice and other rodents have been identified.