Fluorescent cellular biomarkers play an essential role in biology and medicine for in vitro and in vivo imaging in living cells. Recently, we have demonstrated that photoluminescence (PL) can be driven chemically by changing the occupation of NV− and NV0 states by H- or O-termination. In the presented work we study, how the luminescence of NV centers at controlled depth from the surface changes upon different surface treatment. We compare NV luminescence of hydrogen (H) and oxygen (O) terminated surfaces in single crystal diamond (SCD) containing shallow-implanted NV centers (3–10 nm) with similarly treated nanodiamond particles (ND) of various size distributions. The H-termination leads to reduction of NV− related luminescence in both, ND and SCD. The effect is much stronger in ND in comparison with SCD. We mathematically model both situations and discuss parameters influencing the effect, including implantation energy and different contents of nitrogen in the diamond crystal lattice.