The architectural treasures of Zanzibar’s Stone Town, echoing the footprints of ancient civilizations, face an imminent threat of heritage loss due to accelerated material degradation. This underscores the urgent need for an intrinsic examination of building material properties to enhance existing restoration guidelines and effectively safeguard the historical legacy. This study is the first significant step for the extensive procurement of samples to investigate the physical, mechanical, and chemical properties of deteriorating coral stones, mortar, and wood material of Zanzibar’s Stone Town. The results indicate considerable water absorption and varying porosity and densities, highlighting the significant water retention and susceptibility of marine environmental factors. The compressive strength (CS) for coral stone, mortar, and wood falls under 7.6 MPa to 12.2 MPa, 0.5 to 0.9 MPa, and 52.9 to 69.3 MPa, revealing the heterogenous characteristics across the samples. The flexural strength of coral stone and wood was found to be from 2.0 MPa to 3.4 and 72.1 MPa to 98.6 MPa, indicating a high susceptibility to breakage and fracture. Meanwhile, Ultra Pulse Velocity (UPV) averages 1668 to 2070 m/s, revealing void ranges in building materials. Chemical analysis, including X-ray diffraction (XRD) and X-ray fluorescence (XRF), demonstrates higher CaO content in coral stone and mortar, with the predominant mineral aragonite indicating vulnerability to rapid chemical attacks. These results can significantly contribute to future modifications and improvements in restoration guidelines by facilitating the identification and utilization of appropriate materials’ properties. This ensures a high level of compatibility and promotes the sustainable conservation of Stone Town’s architectural heritage.