© The Author(s) 2018. Often, the interpretation of experiments concerning the manipulation of the energy distribution of laser-Accelerated ion bunches is complicated by the multitude of competing dynamic processes simultaneously contributing to recorded ion signals. Here we demonstrate experimentally the acceleration of a clean proton bunch. This was achieved with a microscopic and three-dimensionally confined near critical density plasma, which evolves from a 1 μm diameter plastic sphere, which is levitated and positioned with micrometer precision in the focus of a Petawatt laser pulse. The emitted proton bunch is reproducibly observed with central energies between 20 and 40 MeV and narrow energy spread (down to 25%) showing almost no low-energetic background. Together with three-dimensional particle-in-cell simulations we track the complete acceleration process, evidencing the transition from organized acceleration to Coulomb repulsion. This reveals limitations of current high power lasers and viable paths to optimize laser-driven ion sources.