The effects of thermal treatment and zeolite proton concentration on the chemical state and metal particle size of zeolite Y supported ruthenium (3.0 wt%) have been investigated using H2-TPR, H2-TPD, TPMS, FTIR, TEM, and EXAFS. Heating in Ar of the precursor after ion exchange, [Ru(NH3)6]3+/NaY, up to 400°C leads to nearly 100% autoreduction of the ruthenium, as evidenced by H2-TPR and TPMS. Heating in O2 results in the formation of volatile ruthenium oxides. After autoreduction, the Ru clusters are extremely small, their coordination numbers, derived from EXAFS, are 0.6 for Ru/HY and 0.8 for Ru/NaY. Subsequent treatment at 500°C in flowing H2 induces Ru agglomeration to particles which are about the size of the zeolite Y supercages, as indicated by TEM and EXAFS. The Ru-Ru distances are contracted compared to bulk Ru metal. Washing of autoreduced Ru/NaY with NaOH, thus removing the protons formed during autoreduction, results in Ru agglomeration to large particles (60-100 Å). Comparison of the hydrogen adsorption of Ru clusters with similar sizes of 10-15 Å reveals a marked interaction of the Ru clusters with zeolite protons. Increasing the H+/Ru ratio from 3 for Ru/NaY to 10 for Ru/HY, results in a suppression of hydrogen chemisorption per Ru atom by 75%. The conclusion that formation of metal-proton adducts affects the electronic structure of the Ru clusters, thus being one of the main causes of the lowering of the heat of hydrogen chemisorption, is supported by FTIR data of adsorbed CO. The most pronounced C-O vibration band in Ru/HY is located at 2099 cm-1; this band is absent in Ru/NaY. Significant blue-shifting of the IR bands is in conformity with electron-deficiency of the Ru clusters in Ru/HY. The results confirm that adsorptive properties of zeolite encaged metal clusters can be "tuned" by other ions sharing the same cavities.