Bakers Union Local 3 was established in 1955 with the merger of locals 1, 3, 17, 164, 288, and 579. During the Bakery and Confectionery Workers International Union Convention of 1951, a resolution was passed to implement the merger of all New York bakery locals. Frequent jurisdictional disputes between rival locals were undermining the collective strength of bakers within the industry. Over a dozen local unions representing the interests of workers in the baking industry in New York took part in merger discussions sponsored by the International, but by 1955 only six of the participating unions consented to merge.

Beginning in the 1850s, New York played an important role in the evolution of the unionization of the trade. Owning to the large immigrant presence in New York, unions were originally established according to nationality. The German Bakers, the Jewish Bread Bakers, the French-Italian Bakers, the Spanish Bakers, among others, each existed as separate, independently organized entities. The result of these nationality-organized unions led to a frequent overlapping of jurisdictions within the Greater New York area. As early as 1937, a conference of the Bakery Workers International Union made an effort to address ongoing jurisdiction disputes by encouraging these disparate organizations to unify. Over the course of the next decade a series of mergers took place but nothing compared with the magnitude of the creation of Local 3 in 1955. With its establishment, Local 3 became a dominate force in the baking industry in New York and an important presence on the national front.

Under the dynamic leadership of its first president Frank Dutto, Local 3 would grapple with many challenges. Dutto had risen from the rank and file to become President first of Local 87, then Local 1, and subsequently Local 3. In 1958, Dutto appeared before the McClellan Committee in connection with the sponsorship of a fund-raising dinner for Bakery's vice-president, Max Kralstein. During these hearings Dutto invoked the 5th Amendment when questioned about his affiliation with the Communist Party. Throughout his remaining tenure as president, the taint of these hearings left him vulnerable. Perhaps the greatest upheaval during these years stemmed from corruption charges in the International. In 1958 the Bakery and Confectionery Workers International Union (BCW) was ousted by the AFL-CIO after International President James Cross was indicted for embezzlement. When the AFL chartered the American Bakery and Confectionery Workers' International (ABC), the baking industry fractured on an International level and locally there arose bitter jurisdictional disputes. The mending of this destabilizing division within the International became of primary concern to Local 3 under Dutto's stewardship. Local 3 would remain affiliated with the BCW but at the forefront of efforts to heal the split in the International. In 1959, Local 3 served a vital role in the formation of the Local Unions Reunification Committee. Reunification occurred in 1969 after a twelve-year struggle.

One of the chief concerns of the Local 3 executive board during its early years was the evolution of a standard contract and the development of uniform welfare and pension plans. With the merger of the six unions, Local 3 was now responsible for the negotiation of agreements with over 750 bakery employers each with differing provisions for wages, benefits and shop conditions. The turning point in the establishment of a standard contract came with the general strike of 1959 in which New York locals affiliated with both the BCW and the ABC struck in concert and remained off the job for over 3 months. With the settlement came the first uniform agreement in the baking industry in New York. Within months of the settlement, the union's new headquarters in Long Island City were completed and dedicated in June of 1959. In celebration of the event, Local 3 held its first Cake Show. Cake Shows would become annual events showcasing the talents of the skilled pastry, cake, and bread bakers. These occasions, along with the monthly publication of "Local 3 News," served to organize and bolster the membership of the growing union.

With the death of Frank Dutto in 1969, the former Secretary-Treasurer Harry Rubenstein took over the presidency and served from 1970 to 1973. These years brought a series of new mergers with Local 3 by other unions that sought greater bargaining strength and unity. By the end of Rubenstein's tenure, Matzoh-Noodle Local 269, Jersey Local 167, Bagel Local 338, and Perth Amboy Local 190 had all merged with Local 3. In 1973 the most significant merger since 1955 occurred when the powerful Cake Bakers Union Local 51 merged with Local 3. Jurisdictional disputes that had plagued these rival unions were brought to an end with this merger. Under the terms of the agreement Rubenstein retired and Harry Lorber, former Secretary-Treasurer of Local 51, assumed the position of President of Local 3.

Lorber served as president for the next 16 years, until 1989. Trained as a lawyer, Lorber was a member of the International General Executive Board, chairman of the New York Union Label and Service Trades organization, and chairman of the Baking Industry Labor-Management Apprenticeship Council. In addition he was the chairman of both the Cake Bakers Union Welfare Fund, and of the Local 3 Welfare and Pension Fund. During this era the Union and the baking industry would undergo great changes. Issues related to automation and corporate manufacturing dominated the 1970s and 1980s, as evidenced by the protracted contract negotiations with corporate giants such as Drakes and Entenmann's.

In 1989 Lorber retired and was succeeded by Secretary-Treasurer Ernst Schenkman in December of that year. Following the sudden death of Schenkman in a car accident one month later in January of 1990, the then Secretary-Treasurer Narciso Martas became the fourth President of Local 3.