This study examines the effect of biomolecules on the phase formation, microstructure, water sorption, and compressive strength of carbonated Portland-limestone cement pastes. The chemical analysis was performed using Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), and X-ray diffraction (XRD). Microstructure was examined by using nitrogen adsorption, scanning electron microscopy (SEM), and X-ray microcomputed tomography. At early ages, the addition of biomolecules slightly reduced the carbonation reaction in the pastes. However, at later stages, there was a significant increase in carbonation, attributed to the increased nucleation sites resulting from biomolecule adsorption on the reaction products. FTIR, XRD, TGA, and SEM analyses confirmed that calcite was the dominant polymorph of calcium carbonate in the reaction products. Nitrogen adsorption tests revealed that the capillary pore volume in the pastes with biomolecules was relatively similar to that in the control paste. Micro-CT analysis indicated the presence of a wide range of void structures in the pastes with biomolecules due to the surfactant properties of the biomolecules. Despite having higher void porosity, the pastes with biomolecules exhibited greater compressive strength compared with the control paste. This increased strength is attributed to the biomolecules binding to reaction products and providing adhesion between various phases in the microstructure, enhancing compressive strength at the macro scale. Furthermore, the addition of biomolecules decreased water sorption in the pastes. This reduction is due to increased pore surface hydrophobicity and decreased wettability, leading to reduced capillary forces and consequently lower water sorption in the pastes with biomolecules.