The reconstruction of Bayer was closely linked with the Wirtschaftswunder, or "economic miracle", in the Federal Republic of Germany. As a result of World War II, Bayer for the second time had lost its foreign assets, including its valuable patents. It was clearly vital to rebuild Bayer's foreign business. Thus in 1946, while still under Allied control, Bayer began to reestablish its sales activities abroad. By the 1950s, the company was allowed to acquire foreign affiliates as well. At first the United States and Latin America were the focus of these activities.

The company also expanded its activities in Germany and Europe. In 1957 Bayer joined with Deutsche BP to found Erdölchemie GmbH in Dormagen, thus successfully entering the petrochemical sector. On July 1, 1964, Europe's two largest photographic companies merged to form Agfa-Gevaert AG. In 1967 Bayer's site in Antwerp, Belgium, launched operations.

The foundation for this positive business trend was not only the reestablishment of operations, but also research and development – as it had been at the end of the 19th century. The further development of polyurethane chemistry, new crop protection products, fibers such as the polyacrylonitrile fiber Dralon, the thermoplastic Makrolon®, new dyestuffs for synthetic fibers and many other inventions all contributed to the company's expansion. New products such as cardiovascular medicines, dermal antifungals and broad-spectrum antibiotics emerged from Bayer's pharmaceutical laboratories.

Following the death of Ulrich Haberland in 1961, Kurt Hansen became Chairman of the company's Board of Management. By 1963 – 100 years after its founding – Bayer once again employed nearly 80,000 people and sales had grown to approximately DM 4.7 billion. Further rapid growth necessitated the reorganization of the Bayer Group, which took effect in 1971. A divisional corporate structure replaced the functional organization implemented in the early 1950s.