The presented research shows that the long-term operation of a solid oxide fuel cell can lead to substantial anisotropic changes in anode material. The morphology of microstructure in the investigated stack was observed before and after the aging test using electron nanotomography. The microstructural parameters were estimated based on the obtained digital representation of the anode microstructure. Anisotropy was discovered in two of the three phases that constitute the anode, namely nickel and pores. The third component of the anode, which is yttriumstabilized zirconia, remains isotropic. The changes appear at the microscale and significantly affect the transport phenomena of electrons and gasses. The obtained results indicate that the reference anode material that represents the microstructure before the aging test has isotropic properties which evolve toward strong anisotropy after 3800 h of constant operation. The presented findings are crucial for a credible numerical simulation of solid oxide fuel cells. They indicate that all homogeneous models must adequately account for the microstructure parameters that define the anisotropy of transport phenomena, especially if microstructural data is taken from a post-operational anode.