The scientific and technical Committee (STC) is the part of the organization that works alongside the Permanent Secretariat and the National Focal Points (France, Italy and Monaco). Is is composed by a President, a Head of delegation, five members  for each member of the Agreement and experts. It gives the parties its views and advice on implementing the Agreement. It helps the Permanent Secretariat to prepare resolutions, recommendations, strategy decisions, work programs and international priorities. The Meeting of the Parties formally approves the STC’s proposals with regard to the management plan and priority measures.

The first meeting of the Pelagos Agreement’s STC took place at Monaco’s Ministry of State on October 6, 2006, at the kind invitation of the Government of the Principality of Monaco.

In order to improve the governance of the Agreement, such as established at the VI meeting of the Parties, that took place in Hyères (France) from the 15th to the 16th of December 2015, the STC's Presidency, which was a prerogative of the Principality of Monaco is, every two years and from that moment a rotating one between whichever of the Agreement’s signatory countries. The Presidency of the STC is currently assured by Italy, in the person of Doctor Leonardo Tunesi, Research Director in "Marine biodiversity, Habitat and species Protection" at the "Istituto Superiore per la Protezione e la Ricerca ambientale" (ISPRA).