In 1665, after his expulsion from the Netherlands and as a member of parliament, Downing attached a clause to a bill to fund the war's continuation that specified that the money could only be used for the war effort. This previously little-used move, opposed strongly by Lord Clarendon as an encroachment on the royal prerogative, effectively made permanent the parliamentary appropriation of supplies (meaning that Parliament gained the right to specify that tax revenues should be used only for a particular purpose, rather than spent as the King's government saw fit). In May 1667, in the war's final year, Downing was made secretary to the commissioners of the treasury, his appointment being much welcomed by Pepys, and he took part in the management and reform of the Treasury.