The "National Collection of Industrial Bacteria" was established by the UK Government in the 1950s as a depository for important non-medical bacteria, and was formed as a merger of the existing industrial and marine collections of the UK’s Ministry of Agriculture, Fisheries and Food (MAFF). The collection continued to be part of the Scientific Civil Service for many years, moving to Scotland in 1959, and expanding to include marine, food and novel bacteria. In 1983 management of the collection was transferred to the University of Aberdeen, and the company NCIMB Ltd was created.

NCIMB Ltd received £350,000 investment from E-Synergy in 2001 and 2003. This has enabled the company to develop broader microbiology and chemical analysis capabilities, and to expand its range of commercial services.