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Background Gender-affirming surgical procedures, such as metoidioplasty and phalloplasty for those assigned female at birth, are complex and multistaged and involve risks. Individuals considering these procedures experience greater uncertainty or decisional conflict, compounded by difficulty finding trustworthy information. Aim (1) To explore the factors contributing to decisional uncertainty and the needs of individuals considering metoidioplasty and phalloplasty gender-affirming surgery (MaPGAS) and (2) to inform development of a patient-centered decision aid. Methods This cross-sectional study was based on mixed methods. Adult transgender men and nonbinary individuals assigned female at birth at various stages of MaPGAS decision making were recruited from 2 study sites in the United States to participate in semistructured interviews and an online gender health survey, which included measures of gender congruence, decisional conflict, urinary health, and quality of life. Trained qualitative researchers conducted all interviews with questions to explore constructs from the Ottawa decision support framework. Outcomes Outcomes included goals and priorities for MaPGAS, expectations, knowledge, and decisional needs, as well as variations in decisional conflict by surgical preference, surgical status, and sociodemographic variables. Results We interviewed 26 participants and collected survey data from 39 (24 interviewees, 92%) at various stages of MaPGAS decision making. In surveys and interviews, affirmation of gender identity, standing to urinate, sensation, and the ability to “pass” as male emerged as highly important factors for deciding to undergo MaPGAS. A third of survey respondents reported decisional conflict. Triangulation of data from all sources revealed that conflict emerged most when trying to balance the strong desire to resolve gender dysphoria through surgical transition against the risks and unknowns in urinary and sexual function, appearance, and preservation of sensation post-MaPGAS. Insurance coverage, age, access to surgeons, and health concerns further influenced surgery preferences and timing. Clinical Implications The findings add to the understanding of decisional needs and priorities of those considering MaPGAS while revealing new complexities among knowledge, personal factors, and decisional uncertainty. Strengths and Limitations This mixed methods study was codeveloped by members of the transgender and nonbinary community and yielded important guidance for providers and individuals considering MaPGAS. The results provide rich qualitative insights for MaPGAS decision making in US contexts. Limitations include low diversity and sample size; both are being addressed in work underway. Conclusions This study increases understanding of the factors important to MaPGAS decision making, and results are being used to guide development of a patient-centered surgical decision aid and informed survey revision for national distribution.