We present atomic-scale characterization of site-controlled InAs/InP(001) quantum dots grown by metal-organic chemical vapor deposition using nano-area selective area growth. We have developed for this purpose a process combining e-beam lithography, inductively coupled-plasma etching and focused ion beam etching to isolate a few quantum dots. The size, the shape and the composition of the quantum dots are investigated by Scanning Transmission Electron Microscopy. A comparison with the well-known single self-assembled quantum dots highlights the specificities of our growth mode compared to the Stranski–Krastanov growth mode. ► Structural study of site-controlled quantum dots by Scanning Transmission Electron Microscopy. ► Processing of site-controlled quantum dots for a deterministic observation by transmission electron microscopy. ► Determination of the composition of InAs(P)/InP site-controlled quantum dots by Energy Dispersive X-Ray measurements.