From informal street markets to bars and food stalls illegally built on public land, nothing has been spared, as squads of workers move in toclear the chaos and make the bustling city beautiful again.
But the cleanup has made daily life hard for many in Benin, where the vast majority work in the informal sector.
Like other fast-growing west African urban hubs, Cotonou has vendors selling everything from clothing to fast food by the roadside, and restaurants that spring up all over with their plastic chairs and tables.
"Nature abhors a vacuum," deputy mayor Florentin Tchaou told AFP. "People will take advantage of any empty space to expand their businesses and increase their visibility so as to improve sales."
But in July, freshly elected President Patrice Talon decided it was time to give the country a facelift and gave major cities a six-month deadline to clear their chaotic crowded roads.
Large red crosses were spray painted on building walls due for demolition and posters added warnings that eviction day was near.
Ageline Bocovo, who has been selling clothes in Cotonou for five years, didn't believe it would happen, but was wrong.
"We couldn't fight the police with our bare hands, we had no choice," she said, when, on January 5, she was forced to leave.
Bocovo personally smashed her stall into smithereens, keeping some of the bricks to build a new stall on a smaller street.
"The rest of the rubble will be sold. But it won't bring in much cash," she said.
Armelle Choplin, an urban planner at Cotonou's Research Institute for Development, said the "measure affects the little people, who aren't necessarily organised into associations or unions, as is the case in Anglophone countries like Ghana."
Clearing operations such as this are not uncommon on the continent, where many cities have grown at a rapid rate without much thought about planning.
"Most people welcome it," Choplin said. "It's Haussmann in the tropics," she added, referring to the 19th-century French urban planner best known for transforming Paris into a city of sweeping boulevards.
Africa is expected to account for more than half of the world's population growth between 2015 and 2050 - 9.7-billion - according to a 2015 United Nations report.
That means unchecked activity on public space isn't going to disappear anytime soon.
But the relatively peaceful departure of the squatters in Benin contrasts with neighbouring Nigeria, where clashes with police enforcing eviction notices can lead to violence and even death.
Nevertheless, Cotonou's poor will suffer most by being forced to move stalls to less busy streets at a time when Benin's economy is being hit by recession in Nigeria.
In Ghana's Accra, for example, alternative marketplaces were set up for those evicted. But in Cotonou there is no such relocation or compensation.
So for some, the beautification of Cotonou is a nightmare.
"Where do you want me to go?" asked Eugenie Yovogan, whose small street restaurant stood in front of a government building providing lunch for civil servants.
The clearance robbed her of a prime location and customers. "I lost my clientele forever," she said.
Cotonou's authorities maintain they will support people like Yovogan - even if it's unclear if they have the funds to do so.
"Our citizens have demonstrated a very high social maturity, respecting the laws," said Tchaou.
"Now we must be able to relocate them so that their turnover does not fall. But this requires the means, and sweeping, garbage collection, this is already expensive."
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