The IGSN was developed as part of SESAR with the support of the National Science Foundation at the Lamont–Doherty Earth Observatory. The project was initiated and managed by the Geoinformatics for Geochemistry Program under the direction of Kerstin Lehnert to address data curation obstacles such as different samples that share the same name, and samples that are renamed as they move between laboratories and thus generating analyses that are published under different aliases.  As a result, metadata that ensure unique identification are often missing and this causes irritation for future reuse of data from a sample or the sample itself. Sample databases, such as the SESAR database, are designed to address these issues.
At a workshop hosted at the San Diego Supercomputer Center in 2011, a group of experts met to discuss how to transition the IGSN project into a sustainable infrastructure. The group recommended opening the system to other IGSN registration agents, making it international and transferring the operation and governance of the IGSN to an independent body. This recommendation led to the foundation of the International Geo Sample Implementation Organization e.V. (IGSN e.V.) and the founding event was held at the American Geophysical Union Fall Meeting 2011 in San Francisco, California. The IGSN e.V. is an incorporated organisation under German law and is registered at the Magistrates Court in Potsdam, Germany.
Membership in the organisation is open only to institutions, not to individuals. At present, IGSN e.V. has 16 full members.
In 2018, the Alfred P. Sloan Foundation awarded Columbia University's Lamont–Doherty Earth Observatory a grant for a project to modernise the IGSN business model and system architecture. The funding from the Sloan Foundation will support a series of workshops, at which international experts will come together to redesign the IGSN system and its management to allow researchers world-wide use the IGSN with confidence.
In September 2021, IGSN e.V. and DataCite entered a partnership under which DataCite will provide the IGSN ID registration services and supporting technology to enable the ongoing sustainability of the IGSN PID infrastructure. The IGSN e.V. will facilitate a Community of Communities to promote and support new research and innovation for standard methods of identifying, citing, and locating physical samples. The partnership allows IGSN to leverage DataCite DOI registration services and to focus community efforts on advocacy and expanding the global samples ecosystem.
IGSN and DataCite have a common purpose, and a close relationship in the future will provide mutual benefit to our shared vision of connecting research and identifying knowledge. The partnership brings years of experience across our organizations and communities to scale sample community engagement, develop sample identifier practice standards, and increase adoption globally. In a study published 2023 by [https://www.knowledge-exchange.info/ Knowledge Exchange] it is highlighted that IGSN IDs point to physical objects instead of intellectual property or outcomes (as DOIs mostly do) or their creators. Besides, the report emphasized that the service itself and its organisational framework were developed bottom-up in a sheer community-based effort.