N'Doumbou began his football career at Division 1 Gabonese club AS Sogara. At the age of 12, N'Doumbou departed the country for France joining local club FC Carpentras in the south of France. He later had a stint at Martigues before joining Marseille on a trial. After excelling at the trials, N'Doumbou was offered an aspirant (youth) contract. While in the club's youth academy, he was captain of the Marseille under-17 team that won the 2008–09 Championnat National Under-17 league title. On 18 November 2009, N'Doumbou signed his first professional contract. The contract took effect on 1 July 2011 as the player had to play out the two years left on his élite contract. N'Doumbou made his professional debut on 9 January 2010, five days after his 18th birthday, in a Coupe de France match against amateur club Trélissac.
On 10 August 2011, N'Doumbou joined Orléans on a one-year loan.