Bioimaging and cell labeling using red or near infrared phosphors emitting in the "therapeutic window" of biological tissues have recently become some of the most active research fields in modern medical diagnostics. However, because organic and inorganic autofluorophores are omnipresent in nature, very often the background signal from fluorochromes other than targeted probes has to be eliminated. This discrimination could be available using a time-gated luminescence microscopy (TGLM) technique associated with long lifetime phosphorescent nanocomposites. Here, we report new SiO2 nanostructured particle (50 nm in diameter) embedded luminescent nanosized [Mo6I8(C2F5COO)6]2- metal atom clusters (1 nm in diameter), successfully prepared by the microemulsion technique. This combination provides new physical insight and displays red emission in biological based solution under UV-Vis excitation with long lifetimes of around 17 and 84 μs. Moreover, the nanoparticles can be internalized by cancer cells after surface functionalization by transferrin protein and clearly imaged by TGLM under excitation at 365 nm. The nanocomposites have been mainly characterized by scanning and transmission electron microscopies (SEM and HAADF-STEM), UV-Vis and photoluminescence (PL) spectroscopies.