Presenting himself as a member of a generation for whom "the crimes of European colonisation are indisputable", the 39-year-old French leader, who came under fire during the presidential campaign for calling French colonisation of Algeria a crime against humanity, nevertheless added that there had been "some great things and some happy stories" in that period of history.
Ahead of a Europe-Africa meeting in Côte d'Ivoire on Wednesday and Thursday, Macron said he would be proposing a "Euro-African initiative" against "criminal organisations and people trafficking networks" in the region.
Following the recent revelations of slave markets in Libya, he also promised "massive support for the evacuation of people in danger" from the country.
Macron also presented himself as the champion of African women.
Across the continent "a girl must have the choice whether to marry at 13 or 14", he said, adding that French educational grants will be given to girls as a priority.
Referring to his controversial comment earlier this year on African women having seven or eight children, he said he regretted referring to the question as a "civilisational" problem but not having raised it.
"When you have demographic growth that is continuously higher than economic growth, you never manage to fight poverty," he said. "Demography cannot be decreed but with seven or eight children per woman, are you sure that is the choice of the young woman?"
As demonstrators against his visit erected barricades near the university, Macron said he was in favour of renaming the CFA franc, regarded as a neocolonial relic by its critics.
But he also said it had brought monetary stability, a "good thing", for the 14 countries that use it.
In a region where French troops are working with African armies to fight armed Islamists, Macron declared "We must eradicate the financing of extremism" but said that religious extremism is "sometimes a more redoubtable threat than terrorism because it is widespread, diffuse, everyday and disrupts households and campuses".
"Macron has clearly learnt from his predecessors' mistakes," commented Achille Mbembe, a professor at South Africa's Witwatersrand University. "He was not there to lecture anyone and he has used a positive tone, more business-like.
"One might wish there was more soul or more talk of values in his speech but, clearly, he wants to modernise the relationship between France and Africa, playing also on the fact that he is from a younger generation than his predecessors. Part of this is, of course, a stance but, on the other hand, he did put out a number of very interesting ideas, such as the long-term mobility visas or exchanges between intellectuals. So we'll now have to see if he in fact puts all these in practice."
After meeting Burkina's President Roch Marc Christian Kaboré earlier, Macron promised that French documents relating to the 1987 murder of former president Thomas Sankara will be declassified.
"Thomas Sankara is a very important figure, not only to Burkina but to Africa as a whole and its diaspora," Mbembe told RFI. "Releasing these archives is a long-awaited and very symbolic act. It's a sign of good will on Macron's part and a way to prove he his serious in his willingness to turn the page on Françafrique [France's close relationship with corrupt or authoritarian regimes in its former colonies].
"And we as Africans have to keep him to his promise as seriously as we can, because it's in our own interest too to write a new chapter of France-Africa history."
While insisting that the decision is in the hands of the French justice system, Macron also promised to do "all I can do to facilitate" the extradition of François Compaoré, the brother of deposed president Blaise Compaoré, who is wanted in connection with the 1998 death of journalist Norbert Zongo.