CSIC has been present in Cantabria for several years through the Institute of Physics of Cantabria (IFCA), and in the biology and biomedicine area, through two associated units with the Center for Biological Research (CIB-CSIC) and the Research Biomedical Institute (IIB), respectively. From this initial nucleus, the creation of IBBTEC was proposed, initially under another name, at the end of 2004 by a group of researchers from the Faculty of Medicine of the University of Cantabria (UC).

This proposal, welcomed by the government team of the university, materializes in the creation of a work committee that writes a "supporting memory for the proposal of creation of the Joint Research Center University of Cantabria-CSIC, named Institute of biotechnology and cellular signaling of Cantabria ". After its favorable evaluation by the National Agency of Evaluation and foresight, and the Board of Government of the UC approval, in May of 2006 is presented an extended version of the mentioned memory to CSIC, in which it is already envisaged the possible participation of the Goberment of Cantabria. Once obtained the approval of CSIC, while establishing a negotiating process between the two institutions and the Regional government to determine the conditions of creation and participation in the IBBTEC, an open call is made for the incorporation of researchers from CSIC and from the University of Cantabria to the new institute. This call is assessed and resolved by an international commission of six scientists who, in March 2007, selects the 11 research groups that initially formed part of the IBBTEC.

The process culminates with the publication in the Official Gazette of Cantabria, on April 13, 2007, of the decree establishing at the University of Cantabria a university institute, finally called Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), and with the subsequent signing, on April 17, of the Creation Agreement by the three participating institutions, University of Cantabria, CSIC and IDICAN (public Society of R + D + I of the Government of Cantabria).

With the appointment of the Management committee of the Institute, and a presentation meeting of the researchers of IBBTEC, on May 30, 2007 begins the official activity of the Institute.

Within the process of elaborating the CSIC's strategic plans, IBBTEC presents its own strategic plan in October 2008. Following the corresponding process of analysis and valuation, this strategic plan is approved in the spring of 2009.

In the summer of 2013 opened the new headquarters in the PCTCAN, with 6,000 m2 distributed over five floors. The official inauguration took place on June 17, 2014, and on 24 July the Centre's regulatory agreement was signed by the President of the CSIC, the industry councillor of the Government of Cantabria and the Rector of the University of Cantabria.

Since its creation, IBBTEC has has three Directors: Ángel Pazos, PhD;  Javier León, PhD; and Piero Crespo, PhD, the current director.

Currently, thirteen research groups, divided into two departments, work at IBBTEC.