"The age of Francafrique is well over," Macron said in remarks to the French community in Gabon, referring to France's post-colonization strategy of supporting authoritarian leaders to defend its interests.
Macron's trip, his first to all four countries as President, follows the launch of a new Africa policy and is focused away from France's troubled former colonies in West Africa's Sahel region where anti-French sentiment is rising.
In a speech on Monday, Macron proposed a fresh approach, promising that French military bases in Africa would be co-run with host nations with fewer French troops on the ground.
He also said this week's Africa tour would not be political and his schedule suggests a focus on the environment, culture and scientific research.
While only two of Macron's stops, Gabon and Congo Republic, are former French colonies, some in Gabon's capital Libreville were sceptical of his motives.
"What is Macron doing in Gabon? Is he coming for the forest or to back (President) Ali Bongo?" asked Kevin, a 39-year-old technician who did not wish to give his full name.
"If Macron wants to support the Bongo family, we will rise up," he said. "Gabon is an independent country. It is not France that appoints Gabonese presidents."
Meanwhile in Democratic Republic of Congo (DRC), hundreds protested in front of the French embassy in the capital Kinshasa to denounce France's alleged support for Rwanda, which Congo accuses of backing a rebel group. Rwanda denies this.
Macron is scheduled to fly to Angola on Thursday evening, Congo Republic on Friday and DRC on Saturday.
This report was prepared using Reuters and Agence France-Presse.