Structural characteristics and luminescence properties of B‐doped silicon nanocrystals (Si‐ncs) embedded in a SiO₂ matrix elaborated by ion beam synthesis are investigated. The use of atom probe tomography gives a unique opportunity to experimentally evidence the exact location and composition of B atoms in doped Si‐ncs. These experiments allow to conclude about a favored B location at the periphery of the Si‐ncs depending on their size. In this way, two categories of Si‐ncs can be described: 1) largest Si‐ncs that are B‐doped and where B atoms are located at the Si‐ncs/SiO₂ interface, and 2) smallest Si‐ncs that remain undoped but seem to be surrounded by a B‐rich SiO₂ shell. These structural characteristics (composition and diameters) are correlated to the photoluminescence properties of these Si‐ncs. These measurements show the well‐known quenching of Si‐ncs luminescence due to high B doping, which allows us to conclude about the environment changes brought by the presence of B in Si‐ncs or of B‐rich shell around Si‐ncs.