Istituto Nanoscienze is led by the Director Gaetano Scamarcio, who coordinates the research activities and is in charge of financial, administrative, and technical services. Istituto Nanoscienze has two research sites, one in Pisa (headquarters) and one in Modena, plus a tecnhical support unit in Genova. The head of Modena site is Massimo Rontani.

The Director is supported in his functions by the Institute Board, made of 7 staff members and 2 associate representatives. The Administrative Secretary supervises the financial resources of the whole institute and works in close contact with the Director.