It is presumed that Indigenous researchers are optimally positioned to conduct research about or within their own or other Indigenous communities. However, these researchers may still experience challenges, barriers, and distressing events that are important to identify. Qualitative inquiry may be a particularly vulnerable context for Indigenous researchers given the nature of data collection methods and an emphasis on researcher-participant relationships. This paper details the personal reflections of two American Indian (AI) researchers who carried out qualitative research focused on AI issues and/or communities. The first project examined undergraduate students' opinions of the use of AI imagery in the form of a race-based university mascot. The second was a study of the mental health needs of AI youth and families in an urban community. Several themes characterized both of their experiences and might be generalizable to others working in these contexts: (a) coping with racism and microaggressions; (b) the role and impact of identity politics; (c) community insider/outsider tension; and (d) managing personal distress associated with the research topics and process. These themes are discussed to illuminate ways that Indigenous researchers, engaged in research on Indigenous topics and/or with Indigenous communities, are challenged and affected by their work.