The development of sustainable construction materials can be addressed by incorporating bio-based components, improving energy efficiency, reducing carbon footprint and digitalizing the construction process. This study investigates the design of lightweight 3D printable mortars with reduced contents of cement and two types of microencapsulated bio-based phase change materials (PCM) for architectural applications. An expanded glass lightweight aggregate (EGA) was used for replacing part of the sand to improve the mortar’s thermal insulation capacity. The aim was to design building materials with improved energy efficiency and thermal energy storage capacity. The mortars’ rheological properties were assessed by using a flow table and vane tests. Cement hydration and mechanical properties’ development were monitored with isothermal calorimetry and fresh compression tests. Finally, hardened thermal performance and physical and mechanical properties of the mortars were evaluated. The results of this study could contribute to boost the design of 3D printable mortars with improved thermal performance suitable for architectural applications.