President-elect Trump defeated Democrat Hillary Clinton by 10,704 votes out of nearly 4.8 million ballots cast in Michigan, but Stein alleges that irregularities and the possibility that vote scanning devices could have been hacked call the results into question.
Elections officials in all three states have expressed confidence in their election results.
Michigan's recount could start as early as Friday, though a challenge to the recount by Trump could delay it.
Trump's victory is highly unlikely to be reversed in any of the states, but Stein has said the recount will ensure the integrity of the election.
Republicans have said a Michigan recount would cost taxpayers far more than the $973,000 Stein must pay when filing her recount petition.
Meanwhile in Wisconsin, where Trump defeated Clinton by roughly 22,000 votes, Stein's campaign said Wednesday that it won't appeal a judge's ruling that Wisconsin's recount can be done without counting every ballot by hand.
Stein spokeswoman Margy Levinson said in an email that the campaign decided not to appeal the ruling due to the tight time constraints for completing the Wisconsin recount, which begins Thursday.
Most Wisconsin counties plan to recount their ballots by hand even though the judge's ruling means they can choose to feed the ballots into tabulation machines to double-check the results.
Levinson said Stein's focus will be on verifying the vote on the ground and she encouraged counties to voluntarily conduct a hand recount.
The Wisconsin Republican Party filed a complaint with the Federal Elections Commission on Wednesday alleging that Stein's recount effort amounts to illegal coordination with Clinton designed to circumvent the law and public scrutiny.
Stein campaign manager David Cobb said in a statement that Stein is not coordinating with anyone and dismissed the complaint as a "PR stunt to push a false narrative that will ultimately have no impact on the recount in Wisconsin."
Trump defeated Clinton in Pennsylvania by about 71,000 votes, or about 1 percentage point.
