To bring current thermoelectric (TE) materials achievement into a device for power generation, a full understanding of their dynamic behavior under operating conditions is needed. Here, an in operando study is conducted on the high-performance TE material β-Zn4Sb3 under large temperature gradient and thermal cycling via a new approach using in situ transmission electron microscopy combined with characterization of the TE properties. It is found that after 30 thermal cycles in a low-pressure helium atmosphere the TE performance of β-Zn4Sb3 is maintained with the figure of merit, zT, value of 1.4 at 718 K. Under a temperature gradient of 380 K (Thot = 673 K and Tcold = 293 K) operating for only 30 h, zinc whiskers gradually precipitate on the cold side of the β-Zn4Sb3 leg. The dynamical evolution of Zn in the matrix of β-Zn4Sb3 is found to be the source that leads to a high zT value by lowering of the thermal conductivity and electrical resistivity, but it is also the failure mechanism for the leg under these conditions. The in operando study brings deep insight into the dynamic behavior of nanostructured TE materials for tailoring future TE materials and devices with higher efficiency and longer durability.