The use of biochar as a concrete constituent has been proposed to reduce the massive carbon footprint of concrete. Due to the low density and complex porosity of biochar, microstructural analysis of Portland cement-biochar composites is challenging. This causes challenges to the improvement of the micro-scale understanding of biochar composite behavior. This work advances the microstructural understanding of Portland cement composites with 0, 5, and 25 volume percent (vol%) of cement replaced with wood biochar by applying common characterization techniques of mercury intrusion porosimetry (MIP), gas sorption, scanning electron microscopy, and isothermal heat flow calorimetry (HFC) in conjunction with 1H nuclear magnetic resonance (NMR) and micro-X-ray computed tomography (XCT) analysis techniques. The combination of these techniques allows a multi-scale investigation of the effect of biochar on the microstructure of cement paste. NMR and XCT techniques allow the observation and quantification of the pore space. HFC and MIP confirmed that biochar absorbs moisture and reduces the effective water-cement ratio. Gas sorption, MIP, and NMR shows that 5 vol% replacement does not significantly affect the gel and capillary pore structures. Results from XCT (supported by MIP and NMR) show that biochar can reduce the formation of larger pores. Importantly, XCT results suggest that biochar can act as a flaw in the microstructure which could explain reductions in the mechanical properties. Overall, the mechanical properties already analyzed in the literature are consistent with the microstructural changes observed, and these results highlight the need to carefully tailor the volume fraction of biochar to control its effect on the paste microstructure.