The exclusion of the Soviet Union was indeed a purposeful decision and failing to inform the Soviet government about such an important declaration was a serious diplomatic slight to Moscow. Furthermore, the Atlantic Charter's first three provisions on territorial claims were in part an attempt by Roosevelt to undercut Soviet attempts to win territorial guarantees on the Baltic States and the Polish border from the United Kingdom separate from the United States. Despite the Soviet Union accepting the declaration on September 24th, it continued to cause problems for Anglo-Soviet as well as Alliance diplomacy as a whole.

For context, relations between the three countries were strained when the Nazis invaded the Soviet Union on June 22, 1941. The Soviet Union had been a hostile neutral country, providing massive economic support for Nazi Germany and invading neutral countries. However, the British government had already begun planning for rapprochement earlier that month as it became certain Nazi Germany would invade. Once that occurred, diplomatic outreach was immediate. The initial feelers were awkward but cordial, as the British ambassador Stafford Cripps was back in the UK for consultations. As a result you had two parallel discussions as Cripps and Foreign Secretary Anthony Eden worked with Soviet ambassador Ivan Maisky in the UK while Soviet Foreign Minister Vyacheslav Molotov and Deputy Foreign Minister Andrey Vyshinsky worked with Cripps' substitute, Lacy Baggallay. Generally the Soviet policy was to push towards gaining a political alliance with the UK, military support from the UK and US, and a guarantee that the UK would not pursue a separate peace. The latter point was of greatest concern to Stalin during this period, as he emphasized to Cripps on July 8th. The UK and US also were interested in political and military cooperation, but were restrained by fears of a quick Soviet collapse which persisted until the Battle of Moscow as well as a strong mistrust by the still-neutral US government and public opinion for the Soviet Union.

Nonetheless, despite mutual mistrust efforts got underway for political and military cooperation. Cripps returned to Moscow on June 26 with a military mission and began daily discussions with Molotov, culminating in meetings with Stalin on July 8th and 10th. Anglo-Soviet negotiations culminated in an agreement signed on July 12th on two terms first proposed by Stalin on July 8th. The first term related to the delivery of mutual aid without specifying any numbers and the second that neither country would conclude a separate peace. Konstantin Umansky, Soviet ambassador to the US, also began putting out feelers for military support and avenues for cooperation.

The rest of July saw limited success in the realm of cooperation. Churchill informed the Soviet government on the 21st that it wouldn't be opening a second front in 1941, and only promised 200 fighter aircraft on the 26th. The British government's main focus was preparing for a Soviet collapse and retreat to Siberia, including encouraging the Soviet government to scuttle its navy and destroy its oilfields if it was on the verge of defeat. While July had begun productively, the rest of the month saw the British and Soviet governments struggling to reconcile their different priorities and perceptions.

On the American side, Soviet efforts to produce appreciable results likewise became bogged down in mutual mistrust. While the Americans granted all non-military requests by Umansky on July 3rd, his attempts to secure 3,000 military aircraft were rebuffed. While Roosevelt reasonably pointed out the logistical challenges of such an effort to Umansky on July 10th, the Soviet perception was that "reactionary" US policy was holding back greater support. The main obstacle was the perception by US authorities that the Soviet Union would collapse - Assistant Secretary of State Adolph Berle, for example, put out a memorandum advocating against the sale of anything to the Soviet Union which could be turned over. The Soviet Union's strategy, adopted at the behest of Umansky, was to build strong relationships with friendly individuals such as Harry Hopkins, Secretary of Commerce and a close adviser to Roosevelt, in order to gain access to material aid. The Soviet military mission to the US, dispatched in late July, had largely the same goal. While early attempts to organize a Tripartite Commission to discuss mutual aid foundered, with the Commission only meeting once on August 2nd, Hopkins' successful meeting with Stalin and other Soviet officials on July 30th established the first plans for a conference on economic aid to be held no latter than October of that year in Moscow.

The conference between the US and UK at Placentia Bay, Newfoundland from August 9-12th which produced the Atlantic Charter took place in an environment of deep mistrust between the US, UK, and Soviet Union. Indeed, the origin of discussions about a conference on postwar policy came from an inquiry by British ambassador to the US Lord Halifax on June 15, a week before Germany invaded the Soviet Union, about the US's feelings about a potential Anglo-Soviet agreement on the Baltic states. Adolph Berle, mentioned earlier, quickly pushed for an Anglo-American conference to forestall any such agreements. The UK's pressure on the Polish government in exile to reach a treaty with the Soviet Union even if the terms were unfavorable to Poland caused further alarm in the US. As a result, on July 14th a telegram and verbal message were sent warning against any commitments before a conference. The Soviet Union was purposefully not informed of the conference or involved in the drafting of the charter. However, Roosevelt did try to appease the Soviet Union by not including freedom of religion in the Charter. He had been attempting to work with Umansky to moderate the Soviet's anti-religious policies, with little success, and hoped not including that aspect would ease the most salient disagreement between the US and Soviet Union.

The Soviet Union's reaction to the conference and Charter was outrage. It appeared that its fears of Anglo-American collusion were justified, and that a separate peace might be on the table. Maisky immediately passed a furious message to Eden and refused to declare support for the Charter or meet with the US and UK about postwar reconstruction. While an Anglo-Soviet commercial agreement, signed on August 16th, helped lessen the sting, it was not nearly enough.

But concerns about the Charter did not have as strong a backlash as might be expected as Soviet military fortunes dramatically worsened from late August into September. It became a far more pressing matter, therefore, to secure military support and a Second Front. Fortunately, the Soviet diplomatic push to win over Hopkins had paid off - during the Newfoundland Conference he had convinced Roosevelt of the need for a Three Powers Conference on military aid. Therefore, the first substantial meeting between the three nations was going ahead smoothly. However, at the same time Churchill continued to reject calls for a Second Front, with a particularly definitive rejection on September 16th. While British material aid steadily increased, with another 200 aircraft promised in late August, it hadn't reached the scale desired by Stalin.

In this context, the Soviet government decided to make concessions in order to smooth the path to greater military aid. On September 16th Maisky informed Eden that the Soviet Union would agree to the provisions of the Atlantic Charter, though the decision was likely made around September 13th. In the run up to the first conference between the three powers, smoothing over any public disagreements and presenting a united front was paramount, particularly as the US still remained technically neutral. When the conference opened on September 28th, immediate objections over the Atlantic Charter were set aside.