A method for controlling the purity of hydrogen in a reforming apparatus is described where in the apparatus includes a fuel processor, a purification unit and a system controller. The controller determines a calculated flow of reformate from the fuel processor and operates the purification unit based on the calculated flow. The calculated flow is derived from a process model of the fuel processor and known feed(s) to the fuel processor. The calculated flow of reformate is used to control the flow of reformate to adsorbent beds within the purification unit and can be used to control other materials flows within the apparatus. Means for reducing fluctuations in the pressure and/or flow rate of reformate flowing from the fuel processor to the purification unit are also disclosed. The purity of the hydrogen produced can be maintained by adjusting the operation of the purification unit in response to changes in reformate composition, pressure and/or flow rate.