Abstract This work compares the hydrogen purity and recovery produced by a methanol steam reforming (MSR) packed bed membrane reactor (PBMR) equipped with a membrane selective to hydrogen (Pd-Ag) and with a membrane selective to carbon dioxide (porous membrane filled with ionic liquids-ILs). A 3-dimensional non-isothermal PBMR model was developed in Fluent (Ansys™) for simulating a PBMR equipped with these two types of membranes and simulating a conventional packed bed reactor (PBR). For the development PBMR models a MSR mechanistic kinetic model was fitted to experimental reaction rates of a commercial catalyst (BASF RP60). The results indicated that selective hydrogen removal from the reaction medium originates a significant increase in the methanol conversion, while the carbon dioxide removal has a smaller effect. CO 2 -PBMR showed to be more efficient in terms of energy consumption than H 2 -PMBR. The simulation results showed also that ILs membranes must have a minimum permeance of ⩾1 x 10 −6 mol s −1 m −2 Pa −1 and CO 2 /H 2 selectivity of ⩾200 at 473 K to be attractive for this type of applications. The advantages and limitations of each reactor configuration are discussed based on experimental and simulated data.