Abstract A first series of nitrogen infusion runs of 1.3 GHz single-cell cavities at DESY resulted in an unexpected and severe deterioration observed during the vertical cold test. To investigate the origin of the deterioration, one of the cavities underwent extensive radio-frequency measurements and a temperature- and magnetic field-mapping was performed in collaboration with the Helmholtz-Zentrum Berlin. After combining all results, regions of interests were identified and cut-out of the cavity. Subsequent surface analysis techniques (EBSD, PALS, PIXE, SEM/EDX, SIMS, XPS) were applied in order to identify the microscopic origin of the deterioration and especially the differences between hot and cold spots as well as quench spots. An excess of niobium carbides, reducing the thermal conductivity, was identified as the probable cause for the deterioration, and the size- and density-distributions were observed to be crucial for the resulting performance reduction. The origin for the local differences in the niobium carbide formation between hot and cold spots is an effect of preexisting variations of the crystal structure.