Studying the impact of the protein accessibility level on macronutrient digestion kinetics is highly relevant since it can be utilised to achieve specific digestive responses. In this work, plant-based shakes containing protein with two distinct levels of accessibility were designed. On the one hand, free, non-entrapped protein was added, being pea protein isolate (PPI) dispersions further stabilized by high pressure homogenisation (HPH). On the other hand, individual cotyledon pea cell (IPC) suspensions were considered as source of naturally entrapped protein. The two structural protein organisations were blended. The ratio of protein derived from PPI and IPC was modified as part of this work, yet, the total protein content was kept constant at 6%. The results showed that increasing the IPC content (5% versus 15%) significantly decreased protein as well as starch digestion kinetics. For instance, protein extent decreased from 75% to 68%, and starch extent decreased from 63% to 47%. Moreover, shakes having greater protein digestibility presented also greater starch digestibility which highlights the important role of the protein matrix in modulating starch digestion as part of pulse cells. Finally, introducing individual pea cells in the shakes retarded lipolysis kinetics.This study showed that altering (the ratio of) protein accessibility level in plant-based shakes is a manner to modulate macronutrient digestion kinetics. This is a promising strategy to target specific digestion functionalities.