The bill as it passed the House discriminated in favor of nations with which the United States had commercial treaties. That is to say, it favored France and Holland as against Great Britain, which had the bulk of America's foreign trade. Though Madison insisted on this provision and was supported by a large majority of the House, the Senate would not agree to it. During the early sessions of Congress the Senate met behind closed doors, a practice which it did not abandon until five years later. From the accounts of the discussion preserved in Maclay's diary it appears that there was much wrangling. Maclay relates that on one occasion when Pennsylvania's demands were sharply attacked, his colleague, Robert Morris, was so incensed that Maclay "could see his nostrils widen and his nose flatten like the head of a viper." Pierce Butler of South Carolina "flamed away and threatened a dissolution of the Union, with regard to his State, as sure as God was in the firmament." Thus began a line of argument that was frequently pursued thereafter until it was ended by wager of battle. On several occasions the division was so close that Vice-President Adams gave the casting vote. Although there was much railing in the Senate against imposts as a burden to the agricultural sections, yet some who opposed duties in the abstract thought of particulars that ought not to be neglected if the principle of protection were admitted. Duties on hemp and cotton therefore found their way into the bill through amendments voted by the Senate. Adjustment of the differences between the two houses was hindered by the resentment of the House at the removal of the treaty discrimination feature, but the Senate with characteristic address evaded the issue by promising to deal with it as a separate measure and ended by thwarting the House on that point.

On the whole, in view of the sharp differences of opinion, the action taken on the tariff was remarkably expeditious. The bill, which passed the House on May 16, was passed by the Senate on June 2, and although delay now ensued because of the conflict over the discrimination issue, the bill became law by the President's approval on July 4. This prompt conclusion in spite of closely-balanced factions becomes more intelligible when it is observed that the rules of the Senate then provided that, "in case of a debate becoming tedious, four Senators may call for the question." Brief as was the period of consideration as compared with the practice since that day, Maclay noted indignantly that the merchants had "already added the amount of the duties to the price of their goods" so that a burden fell upon the consumers without advantage to the Treasury. Such consequence is evidence of defect in procedure which the experience of other nations has led them to correct, but which has continued to increase in the United States until it has attained monstrous proportions. Under the English budget system new imposts now take effect as soon as they are proposed by the government, the contingency of alteration in the course of enactment being provided for by return of payments made in error. The general tendency of civilized government is now strongly in favor of attaching the process of deliberation upon financial measures to the period of their administrative incubation, and of shortening the period of formal legislative consideration.

One of the tasks of Congress in its first session was to draught amendments to the Constitution. The reasons for such action were stated by Madison to be a desire to propitiate those who desired a bill of rights, and an effort to secure acceptance of the Constitution in Rhode Island and North Carolina. Promises had been made, in the course of the struggle for adoption, that this matter would be taken up, and there was a general willingness to proceed with it. Under the leadership of Madison, the House adopted seventeen amendments, which were reduced by the Senate to twelve. Of these, ten were eventually ratified and formed what is commonly known as the Bill of Rights.

Apart from this matter, the session, which lasted until September 29, was almost wholly occupied with measures to organize the new government. To understand the significance of the action taken, it should be remembered that the passions excited by the struggle over the new Constitution were still turbulent. Fisher Ames of Massachusetts, a member without previous national experience, who watched the proceedings with keen observation, early noticed the presence of a group of objectors whose motives he regarded as partly factious and partly temperamental. Writing to a friend about the character of the House, he remarked: "Three sorts of people are often troublesome: the anti-federals, who alone are weak and some of them well disposed; the dupes of local prejudices, who fear eastern influence, monopolies, and navigation acts; and lastly the violent republicans, as they think fit to style themselves, who are new lights in politics, who are more solicitous to establish, or rather to expatiate upon, some sounding principle of republicanism, than to protect property, cement the union, and perpetuate liberty." The spirit of opposition had from the first an experienced leader in Elbridge Gerry of Massachusetts. He had seen many years of service in the Continental Congress which he first entered in 1776. He was a delegate to the Philadelphia convention, in whose sessions he showed a contentious temper, and in the end refused to subscribe to the new Constitution. In the convention debates he had strongly declared himself "against letting the heads of the departments, particularly of finance, have anything to do with business connected with legislation." Defeated in the convention, Gerry was now bent upon making his ideas prevail in the organization of the government.

On May 19, the matter of the executive departments was brought up in committee of the whole by Boudinot of New Jersey. At this time it was the practice of Congress to take up matters first in committee of the whole, and, after general conclusions had been reached, to appoint a committee to prepare and bring in a bill. A warm discussion ensued on the question whether the heads of the departments should be removable by the President. Gerry, who did not take a prominent part in the debate, spoke with a mildness that was in marked contrast with the excitement shown by some of the speakers. He was in favor of supporting the President to the utmost and of making him as responsible as possible, but since Congress had obviously no right to confer a power not authorized by the Constitution, and since the Constitution had conditioned appointments on the consent of the Senate, it followed that removals must be subject to the same condition. He spoke briefly and only once, although the debate became long and impassioned. But he was merely reserving his fire, as subsequent developments soon showed. Without a call for the ayes and nays, the question was decided in favor of declaring the power of removal to be in the President. The committee then proceeded to the consideration of the Treasury Department. Gerry at once made a plea for delay. "He thought they were hurrying on business too rapidly. Gentlemen had already committed themselves on one very important point." He "knew nothing of the system which gentlemen proposed to adopt in arranging the Treasury Department," but the fact was worth considering that "the late Congress had, on long experience, thought proper to organize the Treasury Department, in a mode different from that now proposed." He "would be glad to know what the reasons were that would induce the committee to adopt a different system from that which had been found most beneficial to the United States."

What Gerry had in view was the retention of the then existing system of Treasury management by a Board of Commissioners. In 1781 the Continental Congress had been forced to let the Treasury pass out of its own hands into those of a Superintendent of Finance, through sheer inability to get any funds unless the change was made. Robert Morris, who held the position, had resigned in January, 1783, because of the behavior of Congress, but the attitude of the army had become so menacing that he was implored to remain in office and attend to the arrears of military pay. He had managed to effect a settlement, and at length retired from office on November 1, 1784. Congress then put the Treasury in the hands of three commissioners appointed and supervised by it. Gerry was now striving to continue this arrangement with as little change as possible.

When debate was resumed the next day, Gerry made a long, smooth speech on the many superior advantages of the Board system. The extent and variety of the functions of the office would be a trial to any one man's integrity. "Admit these innumerable opportunities for defrauding the revenue, without check or control, and it is next to impossible he should remain unsullied in reputation, or innoxious with respect to misapplying his trust." The situation would be "Very disagreeable to the person appointed, provided he is an honest, upright man; it will be disagreeable also to the people of the Union, who will always have reason to suspect" misconduct. "We have had a Board of Treasury and we have had a Financier. Have not express charges, as well as vague rumors, been brought against him at the bar of the public? They may be unfounded, it is true; but it shows that a man cannot serve in such a station without exciting popular clamor. It is very well known, I dare say, to many gentlemen in this House, that the noise and commotion were such as obliged Congress once more to alter their Treasury Department, and place it under the management of a Board of Commissioners." He descanted upon the perils to liberty involved in the course they were pursuing. Surround the President with Ministers of State and "the President will be induced to place more confidence in them than in the Senate…. An oligarchy will be confirmed upon the ruin of the democracy; a government most hateful will descend to our posterity and all our exertions in the glorious cause of freedom will be frustrated."

Gerry's speech as a whole was tactful and persuasive, but he made a blunder when he appealed to the recollections of the old members, men who had been in the Continental Congress, or else in some position where they could view its springs of action. Their recollections now came forward to his discomfiture. "My official duty," said Wadsworth of Connecticut, "has led me often to attend at the Treasury of the United States, and, from my experience, I venture to pronounce that a Board of Treasury is the worst of all institutions. They have doubled our national debt." He contrasted the order and clearness of accounts while the Superintendent of Finance was in charge with the situation since then. If the committee had before them the transactions of the Treasury Board, "instead of system and responsibility they would find nothing but confusion and disorder, without a possibility of checking their accounts." Boudinot of New Jersey said he "would state a circumstance which might give the committee some small idea of what the savings under the Superintendent were. The expenditure of hay at a certain post was one hundred and forty tons; such was the estimate laid before him; yet twelve tons carried the post through the year, and the supply was abundant, and the post was as fully and usefully occupied as it had ever been before." Of course there was an outcry against the Superintendent of Finance; "he rather wondered that the clamor was not more loud and tremendous." He remembered that "one hundred and forty-six supernumerary officers were brushed off in one day, who had long been sucking the vital blood and spirit of the nation. Was it to be wondered at, if this swarm should raise a buzz about him?" Gerry fought on almost singlehanded, but he could not refute the evidence that he had invited. He lost his temper and resorted to sarcasm. If a single head of the Treasury was so desirable, why not "have a single legislator; one man to make all the laws, the revenue laws particularly, because among many there is less responsibility, system, and energy; consequently a numerous representation in this House is an odious institution."

The case for the Treasury Board was so hopeless that nothing more was heard of it; but the battle over the removal question was renewed with added violence, when the bill for establishing the Department of Foreign Affairs came up for consideration. White of Virginia now led the attack. He had been a member of the Continental Congress from 1786 to 1788, and a member of the ratifying convention of his State. Although he voted for a provisional acceptance of the Constitution, he had supported an amendment requiring Congress to collect direct taxes or excises through State agency, which would have been in effect a return to the plan of requisitions—the bane of the Confederation. In an elaborate speech he attacked the clause giving the President power to remove from office, as an attempt to impart an authority not conferred by the Constitution, and inconsistent with the requirement that appointments should be made with the advice and consent of the Senate. The debate soon became heated. "Let us look around at this moment," said Jackson of Georgia, "and see the progress we are making toward venality and corruption. We already hear the sounding title of Highness and Most Honorable trumpeted in our ears, which, ten years since, would have exalted a man to a station as high as Haman's gibbet." Page of Virginia was ablaze with indignation. "Good God!" he exclaimed. "What, authorize in a free republic, by law, too, by your first act, the exertion of a dangerous royal prerogative in your Chief Magistrate!" Gerry, in remarks whose oblique criticism upon arrangements at the President's house was perfectly well understood, dwelt upon the possibility that the President might be guided by some other criterion than discharge of duty as the law directs. "Perhaps the officer is not good natured enough; he makes an ungraceful bow, or does it left leg foremost; this is unbecoming in a great officer at the President's levee. Now, because he is so unfortunate as not to be so good a dancer as he is a worthy officer, he must be removed." These rhetorical flourishes, which are significant of the undercurrent of sentiment, hardly do justice to the general quality of the debate which was marked by legal acuteness on both sides. Madison pressed home the sensible argument that the President could not be held to responsibility unless he could control his subordinates. "And if it should happen that the officers connect themselves with the Senate, they may mutually support each other, and for want of efficacy reduce the power of the President to a mere vapor; in which case, his responsibility would be annihilated and the expectation of it unjust."

The debate lasted for several days, but Madison won by a vote of 34 to 20 in committee, in favor of retaining the clause. On second thought, however, and probably after consultation with the little group of constructive statesmen who stood behind the scenes, he decided that it might be dangerous to allow the President's power of removal to rest upon a legislative grant that might be revoked. When the report from the committee of the whole was taken up in the House, a few days later, Benson of New York proposed that the disputed clause should be omitted and the language of the bill should be worded so as to imply that the power of removal was in the President. Madison accepted the suggestion, and the matter was thus settled. The point was covered by providing that the chief clerk of the Department should take charge "whenever the principal officer shall be removed from office by the President." The clause got through the Senate by the casting vote of the Vice-President, and a similar provision was inserted, without further contest, in all the acts creating the executive departments. It is rather striking evidence of the Utopian expectations which could then be indulged that Daniel Carroll of Maryland was persistent in urging that the existence of the office should be limited to a few years, "under a hope that a time would come when the United States would be disengaged from the necessity of supporting a Secretary of Foreign Affairs." Although Gerry and others expressed sympathy with the motion it was voted down without a division.