Reinforced concrete structures have a critical durability challenge due to crack formation, facilitating moisture penetration, steel corrosion, and progressive structural deterioration. To address these challenges, this work systematically investigates the synergistic effects of pozzolanic materials in cement mortar and encapsulated healing agents on the autonomous repair capability of sustainable concrete notched beams under flexural loading. In this work, an experimental program consisting of three types of cement mortar with dimensions of 50 × 50 × 220 mm, it was performed using advanced material systems involving pozzolanic additives (silica fume (SF), marble powder (MP) and an encapsulated system incorporating expansive minerals (MgO, CaO, and bentonite) in macro-capsules with a thickness of 0.45 mm, a length of 50 mm, and inner diameters of 6.15 mm and 11.4 mm for the inner and outer capsules, within optimized mortar matrices. Healing efficiency was evaluated via crack area efficiency and load recovery coefficient measurements. Also, advanced microstructure characterization techniques (SEM–EDS, XRD, FT-IR) provided multiscale analysis of healing products and matrix-capsule interfaces to assess healing efficiency. The results showed that SF had superior pozzolanic and healing performance, achieving 87.5% crack sealing and 20% load recovery through increased pozzolanic activity and CSH production. Furthermore, microstructural analyses (SEM/XRD/FT-IR) validated its activity in matrix densification, CH reduction, and interfacial refinement. However, MP mostly acts as an inert filler, revealing the vital performance of SF for self-healing mortar systems. These findings contribute to developing autonomous self-healing technology, providing concrete with an extended service life for sustainable construction applications.