The two-step bubble column-photobioreactor photosynthetic biogas upgrading system can enable simultaneous production of biomethane and value-added products from microalgae. However, due to the influence of a large number of variables, including downstream processes and the presence of microalgae, no unanimity has been reached regarding the performance of bubble column reactors in photosynthetic biogas upgrading. To investigate this further, the present work documents in detail, the design and commissioning of a lab-scale bubble column reactor capable of treating up to 16.3 L/h of biogas while being scalable. The performance of the bubble column was assessed at a pH of 9.35 with different algal densities of Spirulina platensis at 20 °C in the presence of light (3–5 klux or 40.5–67.5 μmol m–2 s–1). A liquid/gas flow (L/G) ratio of 0.5 allowed consistent CO2 removal of over 98% irrespective of the algal density or its photosynthetic activity. For lower concentrations of algae, the volumetric O2 concentration in the upgraded biomethane varied between 0.05 and 0.52%, thus providing grid quality biomethane. However, for higher algal concentrations, increased oxygen content in the upgraded biomethane due to both enhanced O2 stripping and the photosynthetic activity of the microalgae as well as clogging and foaming posed severe operational challenges.