Semiconducting quantum dots (QDs) have potential applications in light-emitting diodes, single-photon sources and quantum computing due to shape-dependent (opto) electronic properties. Atomic resolution 3D-structure determination is important in understanding growth kinetics and improving device performance. 3D-reconstruction of large QDs was reported using characterization techniques like atomic force microscopy, atom probe tomography and tilt series electron tomography, but, still, atomic resolution tomography of QDs, especially those sized below 10 nm, is a challenge. Inline-3D-holography is an emerging and promising technique to perform atomic resolution tomography at low electron doses. In the present study, atomically resolved 3D structures of QDs were reconstructed using inline-3D-holography, implemented on InN QDs (<10 nm) grown on a Si substrate. The residual amorphous glue distorts the exit surface geometry; hence an error correction method was proposed. This is the first experimental evidence of pre-pyramid shaped 3D structure of QDs sized below 10 nm that supports theoretical predictions. © 2021 The Royal Society of Chemistry.