Khumbeni came through the Norwich City Academy, joining at U9 level. He signed his first professional contract with Norwich City on 7 July 2021, penning a one-year deal.[1] Upon the expiration of his deal, he joined Bolton Wanderers on 16 June 2022, linking up with the newly formed 'B' team.[2]
Khumbeni made his Bolton debut on 9 August 2022 in a 5–1 victory against Salford City in the EFL Cup, coming on in the 83rd minute as a substitute for MJ Williams.[3] On 25 May 2023, he signed a new two-year deal with the option of a further year after captaining the B Team for the season.[4]
On 31 January 2024, Khumbeni joined EFL League Two club Morecambe on loan until the end of the season.[6] On 22 May, Bolton confirmed that they had activated an option to extend his contract with the club.[7]