Scientific integrity is necessary for strong science; yet many variables can influence scientific integrity. In traditional research, some common threats are the pressure to publish, competition for funds, and career advancement. Community-based participatory research (CBPR) provides a different context for scientific integrity with additional and unique concerns. Understanding the perceptions that promote or discourage scientific integrity in CBPR as identified by professional and community investigators is essential to promoting the value of CBPR. This analysis explores the perceptions that facilitate scientific integrity in CBPR as well as the barriers among a sample of 74 professional and community CBPR investigators from 25 CBPR projects in nine states in the southeastern United States in 2012. There were variations in perceptions associated with team member identity as professional or community investigators. Perceptions identified to promote and discourage scientific integrity in CBPR by professional and community investigators were external pressures, community participation, funding, quality control and supervision, communication, training, and character and trust. Some perceptions such as communication and training promoted scientific integrity whereas other perceptions, such as a lack of funds and lack of trust could discourage scientific integrity. These results demonstrate that one of the most important perceptions in maintaining scientific integrity in CBPR is active community participation, which enables a co-responsibility by scientists and community members to provide oversight for scientific integrity. Credible CBPR science is crucial to empower the vulnerable communities to be heard by those in positions of power and policy making.