A combination of X-ray computed tomography (CT) and focused ion beam - scanning electron microscopy (FIB-SEM) has been employed to investigate substrate and related surface defects in a niobium coated superconducting radio frequency (SRF) copper cavity. The cavity was manufactured by spinning, with subsequent application of a sputtering-deposited niobium coating (≈40 μm thick) on the internal surface. Before coating, the copper surface was pre-treated in several stages, ending with chemical polishing. CT and FIB-SEM identified furrow defects (≈20 μm deep) in the copper beneath the coating, which originated from the spinning process. The furrows were filled with niobium and contained voids at the Nb/Cu interface that extended a few microns into the niobium coating. The presence of the defects led to similar furrows at the niobium surface. The study revealed the importance of pre-treatment of the cavity internal surface and control of the spinning process to avoid defects that may have deleterious influence on the Q slope and durability of the niobium coating. •Nb-coated Cu SRF cavity examined by combination of X-ray-CT and FIB-SEM.•Furrow and void defects identified at Nb/Cu interface.•Defects at Nb/Cu interface correlated with defects at Nb surface.•Defects in Cu substrate originate from the spinning process of cavity manufacture.