The CCA program aims to build the national and regional capacity that developing countries need in order to fulfil their commitments to the United Nations Framework Convention on Climate Change (UNFCC). The program uses a three-pronged approach of public awareness, technical assistance, and institutional development to achieve this objective.

The Geomatics for Environment and Development Program (GED) applies remote sensing and geographic information systems (RS-GIS) in order to map out social and environmental information that are needed to guide the sustainable development agenda of local communities.

The Instrumentation and Technology (ITD) program aims to develop local instruments and technologies needed to sustain environmental monitoring and research in the country.

The Manila Observatory's many programs come together to explore various aspects of the earth sciences and how these aspects play into the unique culture and communities of the Philippines.

The IGS program is primarily engaged in the scientific observation and analysis of the ionized layer of the earth's atmosphere, which is vital to long range radio communications. Research is based on vertical and oblique (i.e. trans-equatorial) soundings that are routinely conducted together with continuous monitoring of geomagnetic activity.

The Regional Climate Change Systems (RCS) program aims to understand the local or fine-scale features of Philippine climate in order to assess the viability of renewable, climate-based resources for sustainable energy and agriculture, and detect past and future changes that might endanger the survival of local ecosystems and communities.

The SED program aims to monitor and analyze seismic data in order to deepen our understanding of how focal mechanisms operate in the Philippines. Current research focuses on developing theoretical methods to resolve the ambiguity between perpendicular displacements x and y at the source or focus of seismic movements.

The UAQ program aims to provide scientific guidance to air quality assessment and mitigation policy development. It seeks to achieve this through monitoring and modeling activities that form the scientific basis of effective air quality management.