Stones, subject of a big-money transfer bid by Chelsea in the close season, was at fault for the opening goal as Everton lost 2-1 to Swansea City last month and conceded a last-minute penalty in a 4-3 defeat by Stoke City in December.
"John started with the group on Monday and has benefited a lot from the break... I expect him to be part of the squad and to have a very strong ending to the season," Martinez told reporters on Thursday.
Martinez also said there was an "outside chance" new signing Oumar Niasse could make his debut against Bournemouth in the FA Cup on Saturday after revealing the striker underwent a minor surgery for a wrist problem.
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"He had a little surgery on his wrist ... The next 48 hours will give us the final answer on whether or not Oumar will be available," Martinez said.
(Reporting by Shravanth Vijayakumar in Bengaluru, editing by Pritha Sarkar)
