Mr Macron called for "truth and recognition" during a three-day visit that follows heightened tensions between France and Algeria. This year marks six decades of Algerian independence after 132 years of French rule.
European leaders have been struggling to replace Russian energy imports and Algeria, as Africa's top gas exporter, is calling for a role to supply the continent.
A joint commission was announced after Mr Macron's meeting with Algerian President Abdelmadjid Tebboune in Algiers.
The commission will be made up of historians, who will examine the colonial period and the devastating eight-year conflict, in which hundreds of thousand of people were killed.
On Friday, Mr Macron, the first French president to be born after Algerian independence in 1962, dismissed what he said were calls to "choose between pride and repentance".
"I want the truth, and recognition, otherwise we'll never move forward," he said.
He laid a wreath at a monument to those who "died for France" in the mixed Christian-Jewish Saint Eugene Cemetery, a major burial ground for Europeans in colonial times.
French soldiers sang the La Marseillaise as cicadas buzzed in the background.
Mr Macron then visited the Jewish part of the cemetery, accompanied by prominent French Jews.
Later on Friday he was set to meet young Algerian entrepreneurs in Algiers to discuss creating a French-Algerian body to encourage for digital start-ups, as part of a visit his office said would focus on the future.
Mr Tebboune hailed the "promising prospects for improving the special partnership" between the two countries.
Over the years, relations between the two sides have at times been fragile, particularly last year when Mr Macron questioned Algeria's existence as a nation before the French occupation and accused the government of fomenting "hatred towards France".
In response, Mr Tebboune withdrew his country's ambassador and banned French military aircraft from Algerian airspace.
Normal diplomatic relations have since resumed, along with flights to French army bases in Sub-Saharan Africa.
Mr Macron's office insisted gas was not a major feature of the visit, although the head of French energy firm Engie, Catherine MacGregor, was part of his delegation of 90.
The president said on Friday that Algeria had helped Europe diversify its energy supplies by pumping more gas to Italy, which last month signed a deal to import billions more cubic metres via an undersea pipeline from the North African coast.
Dismissing suggestions that Italy and France were "in competition" for Algerian gas, Macron welcomed the deal.
"It's good for Italy, it's good for Europe and it improves the diversification of Europe," he told reporters, noting that France only relies on natural gas for a small part of its energy mix.