In an opinion piece being published around Europe, he calls for the creation of an agency to protect the bloc against cyber-attacks.
Ahead of May's European elections, he advocates a ban on foreign powers financing European political parties.
And he suggests the British people were not properly informed before voting to leave the EU.
Mr Macron set out his proposals for a "European renaissance" in an open letter addressed directly to the "citizens of Europe", which was published in newspapers in all 28 EU member states.
In his letter, Mr Macron says the EU as an institution needs a major shake-up if it is to stop member states "retreating into nationalism" - a direct reference to Brexit.
"Who told the British people the truth about their post-Brexit future?" he asks, using the UK's withdrawal from the union as an example of the EU being in crisis. "Who spoke to them about losing access to the EU market? Who mentioned the risks to peace in Ireland of restoring the border?"
He describes the EU as "not just an economic market" but a "project", before going on to set out his "roadmap for the EU".
In his open letter to Europe, Mr Macron proposes the creation of several new bodies that would oversee change within the EU. They are:
- European Agency for the Protection of Democracies, to protect against cyber attacks, the spread of fake news, and to ban foreign powers from funding European political parties
- European Council for Internal Security, which would comprise a Europe-wide border force agency and asylum office, and a European security council that would have "the UK on board"
- An EU minimum wage, which would be "appropriate to each country" and negotiated collectively on an annual basis, and a guarantee that EU citizens would get "the same pay for the same work"
- European Climate Bank, which would finance the EU's transition to his suggested environmental targets, "zero carbon by 2050 and pesticides halved by 2025"
- A European food safety force, to "improve our food controls" and protect them from the "lobby threat" with "independent scientific assessment of substances hazardous to the environment and health"
- A Conference for Europe, which Mr Macron wants the EU to set up by the end of this year, so that changes can be proposed and approved by representatives from EU institutions and member states
Firstly, Mr Macron says a new European Agency for the Protection of Democracies should be set up to provide each member state with experts who can protect their election processes from cyber-attacks, and manipulation from foreign powers.
"Our first freedom is democratic freedom," he writes. "The freedom to chose our leaders as foreign powers seek to influence our votes at every election."
He then adds that "we should also ban the funding of European political parties by foreign powers".
The French president suggests bringing in new social security measures for EU citizens, including a new "EU minimum wage" that would be "appropriate to each country, negotiated collectively every year".
He also says that the EU should have a "social shield" that would guarantee that workers doing the same job get the same pay.
"[Europe] needs to drive forward a project of convergence rather than competition," he adds.
Mr Macron also proposes new EU-wide environmental targets - "zero carbon by 2050 and pesticides halved by 2025" - which would be financed by a new European Climate Bank.
A new "European food safety force" would enforce the EU's food controls, while funding independent scientific research to combat the influence of corporate lobbies.
"We can't let nationalists with no solutions exploit people's anger," he concludes. "We can't sleepwalk to a diminished Europe... European humanism demands action."