The performance of concrete materials under high pressures and high strain rate loading is critical to their use in protective structures. In this work, we investigated damage in mortar samples subjected to high-velocity projectile impacts to assess performance and deformation mechanisms. Projectile impact tests with 2 mm aluminum (Al) and stainless-steel (SS) spheres were conducted using a two-stage gas gun. Under the same impact energy, the SS projectile induced a larger crater volume which featured a shallow conical crater and a cylindrical tunnel. The Al projectile generated a smaller crater volume which featured a shallower crater without a cylindrical tunnel. High-resolution micro-CT revealed widened horizontal micro-cracks around the SS crater with the intact SS projectile embedded under the tunneling region, while the micro-cracks around the aluminum crater were less obvious. High-resolution micro-CT revealed widened horizontal micro-cracks around the SS crater with the intact SS projectile embedded under the tunneling region, while the micro-cracks around the aluminum crater were less obvious. Based on systematic comparative nanoindentation and scanning electron microscopy in different regions surrounding the crater walls, we inferred that different deformation mechanisms were dominant in samples impacted with SS and Al. In the sample impacted with a SS projectile, the cement regions above the crater depth featured similar indentation properties as those of the pristine mortar, whereas the cement properties below the penetration depth were significantly degraded, indicating pulverization ahead of the projectile trajectory during penetration. In the sample impacted with an Al projectile, cement near to the impact crater featured degraded properties, while cement properties measured at 10 mm beneath the impact surface were comparable to pristine mortar.