The microstructural and compositional homogeneity of La0.99Ca0.01Nb0.99Ti0.01O4−δ and La0.99Sr0.01Nb0.99Al0.01O4−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 La0.99Sr0.01Nb0.99Al0.01O4−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 La0.99Ca0.01Nb0.99Ti0.01O4−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.