The ministers' departure gives Macron a chance to reshape his government without including names who could prove awkward.
Macron accepted her resignation and said he "respected" Goulard's choice.
Ferrand is under investigation over claims he favoured his wife in a lucrative property deal with a public health insurance fund when he headed the company. The former MEP wanted to demonstrate her willingness to cooperate with an investigation into her party's employment of assistants in the European Parliament.
PARIS France's armed forces minister Sylvie Goulard quit the government on Tuesday saying she did not want to be considered in the coming reshuffle because of the investigation overshadowing her party's affairs in the European parliament.
Her resignation comes as Macron carries out a minor shuffle of his government following parliamentary elections on Sunday which handed him and his MoDem allies a commanding majority.
Macron's party won 308 of the 577 seats in Sunday's second round of legislative elections. It is set to be announced Wednesday, with conservative Prime Minister Edouard Philippe staying on.
That followed an announcement late on Monday that Richard Ferrand, an aide to President Emmanuel Macron and minister for territorial planning, facing a separate judicial probe, would leave government for a job as leader of his party in parliament. But she said the possibility of an investigation made it hard for her to stay in the post given Macron's pledge to clean up politics. "This rebalancing exercise must take precedence over any personal considerations", Goulard said in a statement.
"This is why I asked the President, in agreement with the Prime Minister, not to be part of the government anymore".
Since June 9, Modem has been the subject of an investigation into allegations of misuse of public funds.
As justice minister, Mr Bayrou is in charge of promoting a draft law on "restoring trust" in politics.
Observers say her decision puts more pressure to resign on justice minister Francois Bayrou, the founder and leader of Modem. Others in the Republicans staunchly oppose Macron.
He promised to ban politicians from employing members of their family as staff and to ensure they disclose all their personal matters while in office.
Macron is also preparing for his first European Union summit as president on Thursday and Friday.
The proposal stems from the rejuvenated Franco-German leadership in the bloc since the election of Macron whose pro-EU views are shared by German Chancellor Angela Merkel.
OJ Simpson gets July 20 parole hearing date in Nevada
Simpson would go on to be acquitted of criminal murder charges, but be found liable for the deaths in a later civil trial. Added Goldman's sister, Kim Goldman, "He committed a awful heinous crime , and I have no feeling except rot in hell".