Waksman dedicated part of his personal royalties from antibiotics to create the Foundation for Microbiology in 1951. In addition to and separate from the Foundation, he used another portion of the royalty income to establish the Institute of Microbiology to strengthen the study of the field at Rutgers University. The official dedication of the Institute took place in 1954 with Waksman serving as director for its first four years. The new Institute, a free-standing research facility, had well-equipped laboratories and a fermentation pilot plant.

In 1952 Waksman received the Nobel Prize in Physiology or Medicine for "your ingenious, systematic and successful studies of the soil microbes that have led to the discovery of streptomycin." In his speech at the Nobel dinner, Waksman said:

With the removal of the danger lurking in infectious diseases and epidemics, society can face a better future, can prepare for a time when other diseases not now subject to therapy will be brought under control. Let us hope that in contributing the antibiotics, the microbes will have done their part to make the world a better place to live in.²

The Nobel Prize was one of many awards and plaudits that Waksman received in his later years. He died in 1973.