Stein met her life partner Alice B. Toklas on September 8, 1907, on Toklas's first day in Paris, at Sarah and Michael Stein's apartment. On meeting Stein, Toklas wrote:
She was a golden brown presence, burned by the Tuscan sun and with a golden glint in her warm brown hair. She was dressed in a warm brown corduroy suit. She wore a large round coral brooch and when she talked, very little, or laughed, a good deal, I thought her voice came from this brooch. It was unlike anyone else's voice—deep, full, velvety, like a great contralto's, like two voices.
Soon thereafter, Stein introduced Toklas to Pablo Picasso at his studio, where he was at work on Les Demoiselles d'Avignon.
In 1908, they summered in Fiesole, Italy, Toklas staying with Harriet Lane Levy, the companion of her trip from the United States, and her housemate until Alice moved in with Stein and Leo in 1910. That summer, Stein stayed with Michael and Sarah Stein, their son Allan, and Leo in a nearby villa. Gertrude and Alice's summer of 1908 is memorialized in images of the two of them in Venice, at the piazza in front of Saint Mark's.
Toklas arrived in 1907 with Harriet Levy, with Toklas maintaining living arrangements with Levy until she moved to 27 Rue de Fleurus in 1910. In an essay written at the time, Stein discussed the complex efforts humorously, involving much letter writing and Victorian niceties, to extricate Levy from Toklas's living arrangements. In "Harriet", Stein considers Levy's nonexistent plans for the summer, following her nonexistent plans for the winter:
She said she did not have any plans for the summer. No one was interested in this thing in whether she had any plans for the summer. That is not the complete history of this thing, some were interested in this thing in her not having any plans for the summer... Some who were not interested in her not having made plans for the summer were interested in her not having made plans for the following winter. She had not made plans for the summer and she had not made plans for the following winter... There was then coming to be the end of the summer and she was then not answering anything when any one asked her what were her plans for the winter.
During the early summer of 1914, Gertrude bought three paintings by Juan Gris: Roses, Glass and Bottle, and Book and Glasses. Soon after she purchased them from Daniel-Henry Kahnweiler's gallery, the Great War began, Kahnweiler's stock was confiscated and he was not allowed to return to Paris. Gris, who before the war had entered a binding contract with Kahnweiler for his output, was left without income. Gertrude attempted to enter an ancillary arrangement in which she would forward Gris living expenses in exchange for future pictures. Stein and Toklas had plans to visit England to sign a contract for the publication of Three Lives, to spend a few weeks there, and then journey to Spain. They left Paris on July 6, 1914 and returned on October 17. When Britain declared war on Germany, Stein and Toklas were visiting Alfred North Whitehead in England. After a supposed three-week trip to England that stretched to three months due to the War, they returned to France, where they spent the first winter of the war.
With money acquired from the sale of Stein's last Matisse Woman with a Hat to her brother Michael, she and Toklas vacationed in Spain from May 1915, through the spring of 1916. During their interlude in Majorca, Spain, Gertrude continued her correspondence with Mildred Aldrich who kept her apprised of the War's progression, and eventually inspired Gertrude and Alice to return to France to join the war effort.
Toklas and Stein returned to Paris in June 1916, and acquired a Ford automobile with the help of associates in the United States; Gertrude learned to drive it with the help of her friend William Edwards Cook. Gertrude and Alice then volunteered to drive supplies to French hospitals, in the Ford they named Auntie, "after Gertrude's aunt Pauline, 'who always behaved admirably in emergencies and behaved fairly well most times if she was flattered.'"
During the 1930s, Stein and Toklas became famous with the 1933 mass market publication of The Autobiography of Alice B. Toklas. She and Alice had an extended lecture tour in the United States during this decade. They also spent several summers in the town of Bilignin, in the Ain district of eastern France situated in the picturesque region of the Rhône-Alpes. The two women doted on their beloved poodle named "Big Ken" whose successor, "Big Ken's European Vacation", comforted Alice in the years after Gertrude's death.
With the outbreak of World War II, Stein and Toklas relocated to a country home that they had rented for many years previously in Bilignin, Ain, in the Rhône-Alpes region. Gertrude and Alice, who were both Jewish, escaped persecution probably because of their friendship to Bernard Faÿ who was a collaborator with the Vichy regime and had connections to the Gestapo, or possibly because Gertrude was an American and a famous author. Gertrude's book "Wars I Have Seen" written before the German surrender and before the liberation of German concentration camps, likened the German army to Keystone cops. When Faÿ was sentenced to hard labor for life after the war, Gertrude and Alice campaigned for his release. Several years later, Toklas would contribute money to Faÿ's escape from prison. After the war, Stein was visited by many young American soldiers. The August 6, 1945 issue of Life magazine featured a photo of Stein and American soldiers posing in front of Hitler's bunker in Berchtesgaden. They are all giving the Nazi salute and Stein is wearing the traditional Alpine cap, accompanied by the text: "Off We All Went To See Germany."
In the 1980s, a cabinet in the Yale University Beinecke Library, which had been locked for an indeterminate number of years was opened and found to contain some 300 love letters written by Stein and Toklas. They were made public for the first time, revealing intimate details of their relationship. Stein's endearment for Toklas was "Baby Precious", in turn Stein was for Toklas, "Mr. Cuddle-Wuddle".
Stein is the author of one of the earliest coming out stories, "Q.E.D" (published in 1950 as Things as They Are), written in 1903 and suppressed by the author. The story, written during travels after leaving college, is based on a three-person romantic affair she joined while studying at Johns Hopkins in Baltimore. The affair was complicated, as Stein was less experienced with the social dynamics of romantic friendship as well as her own sexuality and any moral dilemmas regarding it. Stein maintained at the time that she detested "passion in its many disguised forms". The relationships of Stein's acquaintances Mabel Haynes and Grace Lounsbury ended as Haynes started one with Mary Bookstaver (also known as May Bookstaver). Stein became enamored of Bookstaver but was unsuccessful in advancing their relationship. Bookstaver, Haynes, and Lounsbury all later married men.
Stein began to accept and define her pseudo-masculinity through the ideas of Otto Weininger's Sex and Character (1906). Weininger, though Jewish by birth, considered Jewish men effeminate and women as incapable of selfhood and genius, except for female homosexuals who may approximate masculinity. As Stein equated genius with masculinity, her position as a female and an intellectual becomes difficult to synthesize and modern feminist interpretations of her work have been called into question.
More positive affirmations of Stein's sexuality began with her relationship with Alice B. Toklas. Ernest Hemingway describes how Alice was Gertrude's "wife" in that Stein rarely addressed his (Hemingway's) wife, and he treated Alice the same, leaving the two "wives" to chat.
The more affirming essay "Miss Furr and Miss Skeene" is one of the first homosexual revelation stories to be published. The work, like Q.E.D., is informed by Stein's growing involvement with a homosexual community, though it is based on lesbian partners Maud Hunt Squire and Ethel Mars. The work contains the word "gay" over one hundred times, perhaps the first published use of the word "gay" in reference to same-sex relationships and those who have them, and, thus, uninformed readers missed the lesbian content. A similar essay of homosexual men begins more obviously with the line "Sometimes men are kissing" but is less well known.
In Tender Buttons Stein comments on lesbian sexuality and the work abounds with "highly condensed layers of public and private meanings" created by wordplay including puns on the words "box", "cow", and in titles such as "tender buttons".