We describe the controlled use of a 17 keV X-ray synchrotron nano-beam to progressively change the oxygen doping level in Bi-2212 superconducting whisker-like single crystals. Our data combine structural and electrical information collected on the same crystals, showing a maximum change in the critical temperature Tc of 1.3 K and a maximum elongation of about 1 Å in the c-axis length, compared to the as-grown conditions. Simulations of our experimental conditions by means of a finite element model exclude local heating induced by the X-ray nano-beam as a possible cause for the change in the doping level and suggest an important role of secondary electrons. These findings support the possible use of hard X-rays as a novel direct-writing, photoresist-free lithographic process for the fabrication of superconducting devices, with potential nanometric resolution and 3D capability.