This work focused on an eco-friendly process to concentrate carotenoids from a citrus juice formulated with clementine and pink grapefruit. It is based on crossflow microfiltration associated with enzymatic liquefaction, diafiltration and pasteurization. The aim was to evaluate the impact of the main operating conditions on the process performance and on the nutritional quality of the final concentrate taking into account the bioaccessibility of β-carotene, β-cryptoxanthin and lycopene. First, the best enzyme/pressure/membrane combination was chosen in order to maximize permeate flux during microfiltration (>100 kg.h−1.m−2 at 2.6 bar with tubular inorganic membranes). Second thanks to a Plackett-Burman experimental design applied to the whole process, we showed the enzymatic dose was the most impacting parameter on carotenoid bioaccessibility and it decreased it. An optimal dose of enzyme had to be defined in order to obtain a good compromise between the process performance and the nutritional quality of the citrus concentrate.