The inscription of unique logo and security marking on diamonds and gemstones is in high demand by worldwide manufacturers and businesses for anti-counterfeiting purposes and traceability. Short pulsed lasers enable marking of transparent materials, challenge remains to produce digital security micro-features on thin facets of the natural diamond in a non-intrusive manner. We propose the design and demonstration of a novel two-lens focusing system to inscribe diamond at microscale and high throughput by an ultrafast laser scanning process. A threshold laser fluence of ∼2.5 J/cm2 and a scan speed of 2 mm/s realized writing of high-contrast data matrix code and serial number without inducing defects and cracking in the diamond. Characterization revealed smooth ablation depth profile with distinct laser-induced periodic surface structures (LIPSS) in the laser inscribed regions determined through scanning electron microscopy (SEM) and 3D optical microscopy. Raman spectroscopy revealed diamond cubic structure dominating with mixing of graphitic structure in the laser markings at various scanning speeds. Comparing with the 0.05 NA f-theta lens, the two-lens focusing system offered 7x improvement in the marking resolution (3 μm in line-width) in addition to its simplicity and add-on flexibility to industrial laser marking systems.