Freeze protection of an on-board emissions treatment substance storage and distribution system in a vehicle includes moving the emissions treatment substance away from a primary fuel/vapor area after filling of the emissions treatment system. In one embodiment an on-board emissions treatment system has a fill tube with a portion extending into a primary fuel fill tube to facilitate co-fueling of the primary fuel and emissions treatment substance. A pressure differential or vacuum is created in the emissions treatment fill tube after filling to move the emissions treatment substance away from a check valve disposed at the terminal end of the fill tube to prevent freezing of the check valve after filling. The emissions treatment substance may be moved out of the co-located portion of the fill tube to an area where passive or active heating of the fill tube may be applied to further reduce susceptibility to freezing.