This "super-program" comprised the various terrestrial biology projects during the first phase of the organization, 1992–1997.

The Forestry Research Program began in 1992 and ran until 1999 when the Foothills Growth and Yield Association was formed conduct the projects.

The GIS program provides an exceptional level of GIS and data management support services for fRI Research.

The fRI Research Grizzly Bear Program provides knowledge and planning tools to ensure the long-term conservation of grizzly bears in Alberta.

The Habitat Suitability Index Program ran from 1994 until 2001.

fRI Research conducted harlequin duck studies beginning in 2000 and completed in 2004.

The program, formerly known as the Natural Disturbance Program, looks at landscape change at a huge scale: Canada's boreal forest.

fRI Research established the Local level Indicators Program in 1997 to assess national criteria for sustainable forest management at a local level. The program ran until 2008.

In 2016, fRI Research hosted a workshop to identify knowledge gaps in migratory bird conservation. This program was launched in 2017 to meet those needs.

The program carries out focused research on infestations of mountain pine beetle in Alberta.

The Northern East Slopes program began in 2000 and ended in 2004.

Occasionally a stand-alone program, and occasionally a component of other programs.