On Thursday Macron paid a visit to an air base in the southwestern city of Istres, addressing the military for the first time since the departure of General Pierre de Villiers.
The general quit on Wednesday after being angered by planned budget cuts to the military and then being publicly rebuked by Macron.
At the air base on Thursday the president, his office said, will “reiterate his support for the armed forces, reminding them of his campaign pledge to increase the defence budget as well as his ambitious plans for them in a difficult international environment”.
Whilst coming in for criticism for his handling of the crisis Macron insisted that he was fully behind the military and has tried to move on from the affair.
On Wednesday, Macron stood by his handling of the disagreement, telling France 2 television that de Villiers was a “fine soldier” it was “not the role” of the chief of staff to question the budget.
The president also reiterated his promise to raise the defence budget again in 2018. “I'm behind our troops,” he assured.
He named General Francois Lecointre, a 55-year-old hero of the Balkans wars, as de Villiers's replacement.
De Villiers, a widely respected figure who had been in the job for three years and was popular with the rank and file, said he had no choice but to stand down.
“I no longer feel able to ensure the sustainability of the model of the armed forces that I think is necessary to guarantee the protection of France and the French people,” he said in a statement.
Uniformed troops formed a guard of honour and applauded de Villiers as he left the defence ministry, according to a one-minute video posted with the message “Merci” (thank you) on the chiefs of staff Twitter account.
Retired general Dominique Trinquand, an adviser to Macron during his campaign, said the row had cast a pall over his otherwise “remarkable” debut.
“This is a hitch that will probably be a bit difficult to get past,” he said in an interview with AFP.