Magnetic skyrmions are stable topological solitons with complex non-coplanar spin structures. Their nanoscopic size and the low electric currents required to control their motion has opened a new field of research, skyrmionics, that aims for the usage of skyrmions as information carriers. Further advances in skyrmionics call for a thorough understanding of their three-dimensional (3D) spin texture, skyrmion–skyrmion interactions and the coupling to surfaces and interfaces, which crucially affect skyrmion stability and mobility. Here, we quantitatively reconstruct the 3D magnetic texture of Bloch skyrmions with sub-10-nanometre resolution using holographic vector-field electron tomography. The reconstructed textures reveal local deviations from a homogeneous Bloch character within the skyrmion tubes, details of the collapse of the skyrmion texture at surfaces and a correlated modulation of the skyrmion tubes in FeGe along their tube axes. Additionally, we confirm the fundamental principles of skyrmion formation through an evaluation of the 3D magnetic energy density across these magnetic solitons.