Crossflow microfiltration was implemented to enrich a clementine/pink grapefruit juice in carotenoids, flavonoids and pectins modulating its sugar content thanks to an added diafiltration step. Using tubular ceramic membrane with pore diameter of 0.2 µm at 30–40 °C, a crossflow velocity of 5 m¿s-1 and a transmembrane pressure of 2.6 bar, the impact of the process was assessed focusing on bioactive compounds and physical characteristics of the concentrates. With permeate flux above 30 kg¿h-1¿m-2, the process resulted in an increase of 8–10 times in the content of provitamin A carotenoids (33 mg¿kg-1 in the final products), lycopene (43 mg¿kg-1), hesperidin (3.2 g¿kg-1) and pectin (5.5 g¿kg-1) giving a unique and interesting composition profile. Moreover, diafiltration divided the sugar content by 3. This can be relevant for the product to be recommended as part of a reduced sugar diet for diabetic people. By modelling the retention of bioactive compounds, we showed that it was possible to modulate sugar, flavonoids, carotenoids and pectin contents in the concentrate that could be a key issue for the biological activity of this potential functional citrus-based food.