Present study investigates the performance and microstructural characteristics of self-compacting concrete (SCC) mixes incorporating limestone calcined clay cement (LC3) as a partial replacement for ordinary portland cement (OPC). The experimental program includes strength, water absorption, sorptivity, chloride permeability, and microstructural analysis of 70 and 40 MPa concrete grades cured for 28, 56, and 90 days. The results show that LC3-based SCC mixes exhibit comparable or superior strength development over OPC mixes at later curing stages (56 and 90 days), owing to the pozzolanic reaction of calcined clay and the formation of durable hydration products such as C–S–H gel and carboaluminate. Durability tests indicate improved resistance to water absorption, chloride ion permeability, and sorptivity in LC3-based SCC, contributing to enhanced long-term performance. Microstructural investigations, including SEM, XRD, and FT-IR analyses, reveal a denser, more refined matrix in LC3 mixes, characterized by a reduced number of voids and a compact interfacial transition zone. The incorporation of LC3 not only improves the sustainability of SCC by reducing carbon emissions and cement consumption but also offers a cost-effective alternative to conventional OPC-based mixes.