The ANR’s core activity is to issue calls for proposals through Programmes. In 2011, 41 calls for proposals were published in all scientific areas. Programmes may consist of a number of calls for proposals, issued within the same year or over a longer period. ANR schemes and programmes can be divided along two lines:
- “Investigator-driven bottom-up programmes” and “Top-down targeted programmes”,
- “Open” programmes and “Public/Private Partnerships” programmes.
- Targeted programmes are the result of a top-down definition process. Responding to economic, environmental and societal demands as well as areas of scientific or technological priority, they accounted for 50% of the agency’s grants in 2011.
ANR's targeted programmes are organised in 6 thematic priorities:
- Bottom-up programmes cater for researchers' creativity through a clear bottom-up process. They account for the other 50% of the agency’s grants.
- Public private partnerships programmes require at least one partner from each sector, public and private.
- Open programmes are open to both public-private partnerships and academic research.
Initiatives carried out by the ANR are organised in three processes:

- Programme Planning defining the content of the calls for proposals each year
- Selection of projects to be funded through peer review in accordance with international standards
- Follow-up and assessment of projects funded; a programme assessment and the dissemination of results when projects have ended.
The 3 processes have received ISO 9001 certification.