The microstructural and compositional homogeneity of La_0.99Ca_0.01Nb_0.99Ti_0.01O_4−δ and La_0.99Sr_0.01Nb_0.99Al_0.01O_4−δ proton conductors was studied using the combination of atomic-resolution scanning transmission electron microscopy (STEM), electron energy loss spectroscopy (EELS) and STEM image simulations. The obtained results revealed that gently doped proton conductors were predominantly composed of grains with a monoclinic lanthanum niobate crystal structure. In addition to the host phase, dopant-rich phases were also observed and identified. The La_0.99Sr_0.01Nb_0.99Al_0.01O_4−δ matrix accommodated dopant-rich grains retaining an LaAlO₃ cubic crystal structure with a significant fraction of Sr incorporated into them. The secondary phases embedded in the La_0.99Ca_0.01Nb_0.99Ti_0.01O_4−δ matrix possessed the pyrochlore La₂Ti₂O₇ crystal structure with Ca partially substituting La. High spatial resolution EELS revealed preferential Ca sites within the pyrochlore La₂Ti₂O₇ crystal lattice. The origin of the secondary phase formation and the role of these phases for the transport properties of co-doped lanthanum niobates are discussed here.