Abstract In Earth’s atmosphere eddy momentum fluxes (EMFs) are largest in the upper troposphere, but EMFs in the lower troposphere, although modest in amplitude, have an intriguing structure. To document this structure, the EMFs in the lower tropospheres of a two-layer quasigeostrophic model, a primitive equation model, and the Southern Hemisphere of a reanalysis dataset are investigated. The lower-tropospheric EMFs are very similar in the cores of the jets in both models and the reanalysis data, with EMF divergence (opposing the upper-tropospheric convergence) due to relatively long waves with slow eastward phase speeds and EMF divergence (as in the upper troposphere) due to shorter waves with faster eastward phase speeds. As the two-layer model is able to capture the EMF divergence by long waves, a qualitative picture of the underlying dynamics is proposed that relies on the negative potential vorticity gradient in the lower layer of the model. Eddies excited by baroclinic instability mix efficiently through a wide region in the lower layer, centered on the latitude of maximum westerlies and encompassing the lower-layer critical latitudes. Near these critical latitudes, the mixing is enhanced, resulting in increased EMF convergence, with compensating EMF divergence in the center of the jet. The EMF convergence at faster phase speeds is due to deep eddies that propagate on the upper-tropospheric potential vorticity gradient.