Bakker played in the youth of AZ, where he won the Tweede Divisie championship with the second team of AZ, Jong AZ, in the 2016–17 season.[1] He made his professional debut in the Eerste Divisie on 18 August 2017, in a 1–3 away win over FC Den Bosch.[2] On 14 December 2016, he was part of the AZ first-team squad for the KNVB Cup match against ASWH, but he did not make an appearance.[3] The following day, he signed a contract extension, keeping him part of AZ until 2020.[3]
On 10 September 2020, Bakker joined Go Ahead Eagles as a free agent on a one-year contract with an option for an extra year.[4] Prior to signing, he had been on a trial with the club and impressed the coaching staff.[5] On 2 October, he made his debut the club in a 2–3 home loss to Jong FC Utrecht as a replacement for the injured starter, Jeroen Veldmate.[6]
On 31 January 2023, Bakker joined Finnish club Kuopion Palloseura on a two-year contract with an option for an extra year.[7] On 24 July 2024, his deal was terminated by mutual agreement, after Bakker had suffered from injuries for over a year.[8]
On 8 August 2024, Bakker signed with Vitesse for two seasons, with an option for a third.[9]
^"Vooruitblik Go Ahead Eagles - Jong FC Utrecht" (in Dutch). Go Ahead Eagles. 1 October 2020. Retrieved 16 October 2020. Jeroen Veldmate heeft tijdens de training een tik tegen zijn been gehad, waardoor Van Wonderen lichte twijfels heeft of zijn aanvoerder morgen aan de aftrap verschijnt. "Zijn kwetsuur is niet ernstig, maar het kan wel een paar dagen pijnlijk aanvoelen voor hem. Indien Jeroen morgenavond niet fit genoeg oogt, dan zal Justin Bakker hem centraal in de verdediging vervangen."