Background Including the lived experience of patients in research is important to improve the quality and outcomes of cancer studies. It is challenging to include adolescents and young adults (AYAs) cancer patients in studies and this accounts even more for AYAs with an uncertain and/or poor prognosis (UPCP). Little is known about involving these AYAs in scientific research. However, by including their lived experiences during multiple phases of research, the quality of the study improves and therefore also the healthcare and quality of life of this unique patient group. We first aimed to document experiences of AYAs and researchers with AYA involvement initiatives using the Involvement Matrix and the nine phases of the research cycle. Second, we aimed to map the (expected) challenges and recommendations, according to patients and researchers, for AYA involvement in each research phase. Methods Thirteen semi-structured qualitative interviews were conducted with AYAs and researchers from February 2020 to May 2020. A thematic analysis codebook with a critical realistic framework was used to analyze the data. Results AYAs and researchers were predominantly positive about AYA involvement within six of the nine phases of research: identify and prioritize topics, develop study design, disseminate information, implement, and evaluate findings. Not all respondents were positive about AYA involvement in the following three phases: formulate research questions, conduct research, and analysis and interpretation. However, few respondents had experience with AYA-researcher collaborations in multiple phases of the research cycle. Last, the results indicate the importance of adding a role (practical support) and two phases (grant application and recruitment) to the Involvement Matrix. Conclusion Our results show the added value of AYA (with a UPCP) involvement within scientific research projects. We recommend researchers to actively think about the level and phase of collaboration prior to each research project, by involving and brainstorming with AYAs at the conception and throughout research projects. Besides, to enhance fruitful participation, we suggest thoroughly discussing the pros and cons of collaboration for each phase together with AYAs via the proposed Involvement Matrix to support transparency. We recommend to report experiences, choices, and results of AYA involvement.