Composite membranes formed of zeolitic fillers embedded in Nafion can be made by evaporating the solvents from a suspension of small zeolite crystals in a Nafion solution. Two natural zeolites were selected as fillers: chabazite and clinoptilolite. Membranes with various zeolite content were obtained. Composite membranes with zeolite content up to 40 vol.% exhibited uniform distribution of the zeolite fillers throughout the thickness, as ascertained by scanning electron microscopy (SEM), energy dispersive X-rays absorption (EDX) and ion conductivity measurements. Although more brittle than Nafion, these composite sheets retain—when hydrated—reasonable flexibility below 40 vol.% zeolite content. We have determined the hydrogen ion conductivity and the permeability of methanol molecules through these membranes (in the H+-form as well as in the Na+-form) in the temperature range 22–60°C. We found that the presence of the zeolitic fillers in the membranes can bear notable changes of conductivity, permeability and selectivity with respect to membranes made out of sole Nafion.