Turkey was hoping to warm frosty relations with Europe during Erdogan's trip to Paris, but the talks were overshadowed by concerns over Turkey's huge crackdown after a 2016 failed coup.
Macron said there was no chance of Turkey's membership bid, which has been languishing for years, moving forward.
"I'd be lying if I said we could open new chapters," he said in reference to the accession process.
"As regards recent relations with the European Union, it is clear that recent developments and choices allow no chance for progress in the process," Macron said after what he described as "very frank" talks with Turkey's strongman.
He emphasised however that he wanted to see Turkey "remain anchored to Europe".
Erdogan said that Turkey's 54-year wait to join the EU was "seriously exhausting" the Turkish people and that he might be forced "to take a decision."
He did not specify what that might be but admitted: "We don't really have an attitude of 'let us in' (to the EU) anymore."
It came after a year in which Turkish-European relations hit a low point, with Erdogan notably accusing Chancellor Angela Merkel of "Nazi practices" for refusing to let his ministers campaign in Germany.
Macron's invitation to Erdogan drew sharp criticism from the French left, trade unions and rights groups, and a group of Kurdish demonstrators who attempted to demonstrate outside the Elysee Palace on Friday were arrested.
The Reporters Without Borders group protested outside the Turkish embassy in Paris, holding aloft stencilled portraits of imprisoned journalists.
Tensions spilled over during Erdogan's meeting with the French press when a journalist pressed him on a report that Turkish intelligence services shipped arms to radical groups in Syria.
"Do not speak with the mouth of FETO," Erdogan retorted, referring to the Fethullah Terror Organisation -- the term Ankara uses for the movement of US-based cleric Fethullah Gulen, whom Turkey accuses of being behind the failed coup as well as the Syria arms report.
Macron chided Erdogan over his rights record.
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