Despite more autism research taking place than ever before, there is a disconnect between the current landscape of autism research and what autistic people and their allies want from research. While participatory research has been proposed as a potential solution, we know little about how researchers (particularly, early career researchers) employ this approach. We interviewed 25 researchers (14 early career and 11 established researchers) about their views and experiences of participatory autism research. Through reflexive thematic analysis of interview and focus group data, we identified three themes. First, our participants emphasised the flexible nature of participatory research, and the many forms it can take; yet noted that this flexibility could cause confusion. Second, our participants highlighted the importance of building relationships with research partners, while commenting on the challenges around effective communication and working with diverse groups of people who may have limited research experience. Finally, participants described the challenges of working within academic environments that are not conducive to participatory research (e.g. due to limited time, funding and support). We discuss these issues with regard to changes required at both an individual and systemic level, ensuring that efforts are made to meaningfully involve autistic people and their allies in all stages of the research process.