The role of NH4+ion confinement in the catalytic etherification of HMF (5-hydroxymethylfurfural) with ethanol to biodiesel additives was evidenced by studying the catalytic behavior of NH4+-Beta zeolites with SiO2/Al2O3ratios of 25 and 75. In order to affect the strength and distribution of the acidic sites, as well as the mobility of NH4+ions in the zeolites cages, a secondary level of porosity was introduced in the NH4+-Beta, presenting a different stability versus alkaline treatment, by using a thermal or an ultrasound assisted method. By analyzing the catalytic behavior in these two series of samples with respect to the changes in porosity by nonlocal density functional theory, structure by XRD, amount of acid sites by FT-IR and mobility of NH4+cations by measurements of reversible NH4+exchange capacity, was evidenced a decrease in catalytic performances both in terms of rate of HMF depletion and productivity to the main products, when confinement of the ammonium ions is lost due to the introduction of mesoporosity. The high capability of ammonium ions release, associated to the mono-dentate configuration, and the minor confinement effect inside the zeolite pore system, due to the more opened pores structure of mesoporous zeolites, hinders both the direct etherification of HMF to EMF [5-(ethoxymethyl)furan-2-carbaldehyde] and the parallel reaction pathway via acetalization, favoring the rapid desorption of the HMFDEA [5-(hydroxymethyl)furfural diethyl acetal] product out of the crystal and the consequent inhibition of the consecutive reactions to EMFDEA [5-(ethoxymethyl)furfural diethyl acetal] and EMF.