The Indomitable Lions, who lifted the trophy on Sunday after beating Egypt 2-1 in the final in Gabon, attended a ceremony in Yaounde on Wednesday.
They presented the Nations Cup trophy to President Biya at Unity Palace.
Later, they travelled in open-top vehicles through the streets of the capital to parade the trophy to fans.
Cameroon's players were given medals by the president, who said their victory should be celebrated by Cameroonians as one nation.
At the end of the ceremony Cameroon First Lady Chantal Biya posed for a series of photos with the players - at one point she used Fabrice Ondoa's phone to take a 'selfie' with them.
Cameroon's success in Gabon ended a 15-year wait to win the tournament again and gave them their fifth title.
The country will host the next edition of the Nations Cup in 2019.

Wardrobes, beds, sofas, lamps and other pieces from the Athletes' Village in Dalmarnock will be handed over to Glasgow Housing Association (GHA).
It will then be passed on to people and charities helping to furnish homes.
About 36,000 items are to be distributed after the Games.
Some of the furniture will have been used by the likes of Sir Bradley Wiggins, Mo Farah, Eilidh Child and possibly Usain Bolt.
It includes items that were previously used at the London 2012 Olympic and Paralympic Games and relocated for use in Glasgow alongside newly-manufactured furniture such as folding chairs and tables.
The plan to pass them on to GHA is part of the legacy programme from Glasgow 2014.
About 700 houses in the Athletes' Village will be sold or rented after the Games, and a new 120-bed care home for the elderly will also be established on the site.
Glasgow 2014 chief executive David Grevemberg said: "It's fantastic that the furniture used by the athletes and officials during the Games this summer is going to be distributed to families in need in Glasgow.
"Sustainability is very high on Glasgow 2014's agenda and this is a tangible benefit from the Games to the great people of this city, following the excitement of the sporting events themselves."
Twelve new training positions at GHA will be created to move and refurbish furniture items.
Olga Clayton, director at Wheatley Group, which runs GHA, said: "We're delighted to support the Commonwealth Games coming to Glasgow and to do our bit to provide a lasting legacy for the people of this city.
"We know many people are finding it difficult financially in these tough times.
"This project will make a big difference to thousands of adults, families and groups who need help to make their house a home."
Cameroon's Africa Cup of Nations-winning squad have been given a special state reception by the country's president Paul Biya.
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Furniture used by some of the world's top athletes during the Commonwealth Games is to be distributed to vulnerable families in Glasgow at the end of the event.