Design of oxide and nanocomposite materials with high mixed protonic-electronic conductivity such as lanthanide niobates and tungstates is encouraging approach in developing hydrogen separation membranes. This work aims at elucidating the relation of structure, oxygen and protonic mobility of such materials. La0.99Ca0.01NbO4, LaNb3O9 and Nd5.5WO11.25−δ were synthesized by Pechini and citrate route. Nanocomposites with LaNb3O9 and Ni + Cu were prepared by ultrasonic dispersion or mechanical treatment in a high energy mill and wet impregnation, then sintered using conventional thermal sintering and hot pressing. All obtained materials were characterized using XRD, SEM, TEM with EDX analysis, IR and Raman spectroscopy. The oxygen and proton mobility were studied by isotope exchange, unit cell volume and weight relaxation techniques. The proton conductivity was studied by Van der Pauw technique. The main phases were scheelite for La0.99Ca0.01NbO4, perovskite for LaNb3O9 and fluorite for Nd5.5WO11.25−δ, extended defects were observed agreeing with IR and Raman spectroscopy data. The oxygen mobility studies revealed two types of bulk oxygen related to two phases in samples. D2O exchange studies demonstrated very fast protonic transport in samples. H2O desorption experiments revealed the working temperature range being 300–450 °C. The protonic conductivity values (~10−4 Ω−1 cm−1 at 400 °C) agree with the literature data and are sufficiently high for the practical application. Proton tracer and chemical diffusion coefficients values are ~10−11 and ~10−3 cm2/s at working temperatures, respectively. Successful test of proton conducting membrane with Nd5.5WO11.25−δ based functional layer showing promising performance has been carried out.