The coup against Niger's President Mohamed Bazoum is the third such putsch in the region in as many years, following similar actions in Mali and Burkina Faso in 2021 and 2022 that forced the pullouts of French troops.
But the Niger coup is particularly bruising for Macron after he sought to make a special ally of Niamey, and a hub for France's presence in the region after the Mali coup.
The situation presents Macron with a string of dilemmas as he retreats to the French presidential Mediterranean residence of Fort Bregancon for a summer holiday that is set to be dominated by the crisis.
In December 2018, Macron vowed that France would remain engaged in the fight against jihadists in the Sahel region of Africa "until the victory is complete", a vow that now appears on shaky ground.
"History repeats itself, the setbacks are accumulating," Pascal Boniface, director of the French Institute of International and Strategic Affairs, told AFP.
"If the putschists stay in power in Niamey, it will be very difficult to leave our soldiers there."
- 'Bet everything' -
France has 1,500 soldiers posted in Niger, and another 1,000 in neighbouring Chad.
The military said this week that evacuating soldiers from Niger -- as was the case with civilians -- was "not on the agenda".
And unlike Mali and Burkina Faso previously, the junta in Niger has not put into question defence agreements with Paris so far.
But "it is a mistake to have bet everything on Niger and Chad" for redeploying French troops after the Burkina and Mali coups, said Francois Gaulme, researcher at the French Institute of International Relations.
He also said the departure of French soldiers from Niger was "inevitable" if the putschist General Abdourahamane Tiani remained in place.
The Le Monde daily described the coup as a "new heavy blow" for France's military strategy in the Sahel region.
"Paris had placed Niamey at the heart of its fight against jihadist groups on a regional scale. With the coup, the entire French strategy could be called into question."
- Actions not words -
Macron -- the first French head of state to be born after former French colonies won independence -- had in 2017 in a famous speech in Ouagadougou vowed a new approach towards the continent.
Since then, he has repeated pleas for a change of method, a partnership of equals, telling magazine Jeune Afrique in 2020 that "between France and Africa, it must be a love story".
But anti-French sentiment in the region has only continued to rise, often whipped up by Russia which over the last years has taken an increasingly prominent presence through the Wagner mercenary group.
Hundreds of people backing the coup protested on Thursday in Niamey's Concertation Square to mark the country's 1960 independence from France, some brandishing giant Russian flags.
Last week thousands of demonstrators gathered outside the French embassy in Niamey, chanting anti-French slogans and waving Russian flags. Paris then ordered the evacuation of its nationals which is still in progress.
Analysts say Macron himself bears some responsibility, even if other factors are also at work.
"He has been criticised since his first five-year term for being arrogant, especially in his relations with certain African heads of state," Gaulme said.
He said the problem above all lies in the gulf between "words and acts" as despite the strong statements "the French system has in fact not changed as it remains focused around military bases and development aid."
- 'Very mobilised' -
Macron "remains very mobilised", an Elysee source said on Tuesday, adding he was talking with regional and European partners "to look at different ways to get out of the crisis".
A French diplomatic source, who asked not to be named, said France was taking several actions to have a less military focus in relations with Africa, notably fighting poverty and global warming while encouraging growth.
"Emmanuel Macron wanted to make an ambitious reset in our relationship with African countries. All of this can only be done over the long term," said the source.
Macron organised in Paris in June a summit on a new global financing pact that is to be at the centre of such efforts.
He notably hosted Bazoum at the Elysee Palace for bilateral talks on the sidelines of that summit.
"We must go beyond the anti-Macron obsession if we want to make a correct analysis of the situation", said the Cameroonian intellectual Achille Mbembe, who teaches history and political science at the University of the Witwatersrand in Johannesburg.
"We are facing a historic backlash which relates to the failure of decolonisation".
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