All agreements are issued with entities whose specific goals or concerns meet the museum's. They aim to join efforts, material and human resources with scientific and technical knowledge in order to develop side-by-side actions that contribute to investigate, train and inform about the cultural and natural heritage of the country, as well as its publication, conservation and protection.

Following are some of such alliances:

National Treasury: National project that includes the museum and seeks to carry out all payments by means of the Generation of Electronic Transactions (GTE, initials in Spanish) system.

Ministry of Finance: The Figure Consolidation System for Public Offices (SICCNET, initials in Spanish) is an electronic information system that stores all budgets, cash flows, bank conciliations, financial investments and degree of employment.

National Comptroller's Office: Information System on Public Budget (SIPP, for its Spanish initials) allows Comptroller's Office to keep updated with all public entities and their budget information.

• Centro Científico Tropical [Tropic Scientific Center]
• Museos del Banco Central [Central Bank Museums]
• Museo de los Niños [Children's Museum]
• Museo Calderón Guardia [Calderon Guardia Museum]
• Museo Histórico Cultural Juan Santamaría [Juan Santamaria Historic and Cultural Museum]
• Museo Omar Salazar , in Turrialba [Omar Salazar Museum]
• Municipalidad de Osa [Municipality of Osa]
• Centros Educativos [educational institutions]