Born in Porto-Novo (a French protectorate in present-day Benin) to a wealthy father and a mother who belonged to the royal family of the Kingdom of Dahomey, he was sent to France for education at the age of 13.

There he received a law degree, medical training, and served in the French armed forces as an army doctor during World War I.

Following the war, Houénou became a minor celebrity in Paris; dating actresses, writing books as a public intellectual, and making connections with many of the elite of French society.

In 1923, he was assaulted in a French nightclub by Americans who objected to an African being served in the club; the attack changed his outlook on issues and he became more active in working against racism.

His father, Joseph Tovalou Quénum (d. 1925), was a successful businessman along the coast and his mother was a sister of the last independent king of Dahomey, Béhanzin.

[3] In 1900, Joseph took two of his sons to Paris for the Exposition Universelle or World's Fair and while there decided to enroll Houénou and his half brother at a boarding school in Bordeaux.

[2] In 1915, Houénou was given French citizenship,[2] an extremely rare status in colonial Africa for people of African descent at that point, with fewer than 100 being citizens of France by 1920.

[2] Houénou became involved with the French intellectual scene and tried to be active as a public intellectual, including the 1921 publication of a scientific study of phonetics and linguistics titled L’involution des métamorphoses et des métempsychoses de l’Univers – L’involution phonétique ou méditations sur les métamorphoses et les métempsychoses du langage.

[5] His interest in Dahomey led him to form the organization Amitié franco-dahoméenne in 1923 in order to promote gradual reform of the French colonial administration.

[11] While denouncing the Americans, the French press elevated the status of Kojo significantly, referring to him in one incident as "a kind of colored Pascal.

'Association' under present terms is but thinly disguised slavery" After the El Garòn incident, Houénou became, in the words of historian Patrick Manning, the "most devastating African critic of the French colonial order.

A libel verdict in favor of Blaise Diagne against charges written by René Maran in Les Continents effectively bankrupted the newspaper and publication ceased in December 1924.

[18] After returning from the UNIA meeting in 1924, Houénou was forced to leave France by the authorities and only allowed to reenter Dahomey in 1925 if he renounced the philosophies of Marcus Garvey, which he did.