The dissipation of heat generation has been one of the largest obstacles in the design of semiconductor devices and reducing the thermal conductivity is vital for improving thermoelectric efficiency. This work focuses on the Bi doping effect on ZnO, and ZnO:Al thin films produced by magnetron sputtering with thickness varying between 500 and 900 nm. The approach introduces Bi ions, a higher mass element, into the ZnO metal-oxide matrix, to hinder phonon-mediated heat conduction and, consequently, reduce thermal conductivity. Atom probe tomography (APT) was employed to survey Bi doping distribution in ZnO:Al:Bi and ZnO:Bi thin films and to study the morphology of the grain boundaries. The thermal properties of the thin films were measured by frequency-domain thermoreflectance. Based on thermal conductivity results, it is concluded that the doping of ZnO films with Al has a significant effect on thermal conductivity, being reduced from 6.0 W m$^{−1}$ K${^−1}$ in its undoped state to 3.3 W m$^{−1}$ K$^{−1}$ for ZnO with ∼3 at.% of Al, mainly due to alloy scattering of phonons in the wurtzite cell. Further doping with Bi contributes to a slight reduction in the thermal conductivity of ZnO:Al.Bi films (2.9 W m$^{−1}$ K$^{−1}$), due to grain boundary scattering by Bi/Bi$_2$O$_3$ phases. This result is understood as the confluence of two counteracting effects. On the one hand, the thermal conductivity of the film decreases because Bi, unlike Al, is segregated to grain boundaries and does not substitute Zn in the wurtzite crystal lattice, which is unequivocally demonstrated by APT results. On the other hand, the simultaneous presence of Al and Bi triggers a morphological change with the film's microstructure becoming more columnar. This change in microstructure from 3D island growth in ZnO:Al and ZnO:Bi to a more regular columnar structure in ZnO:Al,Bi limits further reduction in the thermal conductivity.