The property of persistent luminescence shows great potential for anti-counterfeiting technology and imaging by taking advantage of a background-free signal. Current anti-counterfeiting technologies face the challenge of low security and the inconvenience of being limited to visible light emission, as emitters in the NIR optical windows are required for such applications. Here, we report the preparation of a series of Zn1+xGa2−2xSnxO4 nanoparticles (ZGSO NPs) with persistent luminescence in the first and second near-infrared window to overcome these challenges. ZGSO NPs, doped with transition-metal (Cr3+ and/or Ni2+) and in some cases co-doped with rare-earth (Er3+) ions, were successfully prepared using an improved solid-state method with a subsequent milling process to reach sub-200 nm size particles. X-ray diffraction and absorption spectroscopy were used for the analysis of the structure and local crystal field around the dopant ions at different Sn4+/Ga3+ ratios. The size of the NPs was ~150 nm, measured by DLS. Doped ZGSO NPs exhibited intense photoluminescence in the range from red, NIR-I to NIR-II, and even NIR-III, under UV radiation, and showed persistent luminescence at 700 nm (NIR-I) and 1300 nm (NIR-II) after excitation removal. Hence, these NPs were evaluated for multi-level anti-counterfeiting technology.