Time-resolved luminescence decays of intercalated compounds of hydrogen uranyl phosphate (HUP) with p-toluidinium (HUPPT), benzylaminium (HUPBZ), α–methylbenzylaminium (HUPMBZ) and hydroxylaminium (HUPHAM) were studied. The prepared compounds belong to the tetragonal P4/ncc space group and showed 00l reflections shifted to lower angles relative to HUP, indicating that the intercalation increases the c parameter of the unit cell. The luminescence decays of the compounds with 100% of intercalation ratio (HUPHAM and HUPBZ) were analyzed by Global Analysis, assuming Lianos’ stretched exponential as the model function, which can be applied to compounds with restricted geometry and mobile donor and quencher molecules. It was remarkable that the luminescence decays showed that the quenching of the emission of the uranyl ions by the intercalated protonated amines is not restricted by low dimensionality of the host uranyl phosphate, and that a diffusion mechanism occurs. Benzylaminium cation efficiently quenches the excited energy of the uranyl ions at close distance, but the long-range and long-lifetime quenching is hindered. A different situation is found in the case of the small hydroxylaminium cation, where the long distance diffusion of the species is fast, playing an important role in the quenching of the excited uranyl ions at longer times.