The increasing focus on sustainable construction has driven interest in 3D printing technology, particularly in developing bio-based cementitious composites that incorporate agricultural by-products. This strategy aims to improve the performance of printable materials while promoting an innovative solution for eco-friendly building practices. In this context, this paper investigates the effect of rice husk bio-aggregates on fresh properties, mechanical strength, and microstructure of 3D printable bio-based cementitious composites. A reference mortar was prepared with 0–0.6 mm natural sand and 0.38 water-to-cement ratio. Different volume fractions of rice husk were used (15%, 20%, and 25%). Rheological properties over time were assessed using fresh compression tests, while mechanical properties were evaluated through uniaxial compression tests, on both mold-cast and printed samples. Microstructure and porosity were analyzed using optical microscopy. The results demonstrated that rice husk increases the green strength, critical time, and structuration rate of the composites. Mechanical tests indicated that the addition of rice husk negatively affects compressive strength, due to an increase in porosity and debonding between the rice husk and the matrix. The findings indicate that the rice husk volumetric fraction should be carefully selected to optimize the rheological properties without excessively compromising the mechanical performance of cementitious composites for 3D printing.