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 Background: Studies comparing outcomes following gender-affirming care between autistic and non-autistic individuals with gender dysphoria (GD) are scarce.Objective: To assess whether gender-affirming hormone therapy (GAHT) and top surgery reduce symptoms of gender incongruence (GI) and GD and enhance body satisfaction, and to examine if these associations are influenced by autistic traits or autism diagnosis.Design: Multicenter longitudinal cohort study within a target trial emulation framework (TTE).Setting: The Swedish Gender Dysphoria Study recruited 514 participants from six specialized gender identity clinics in Sweden between 2016 and 2022, with up to a three-year longitudinal follow-up.Participants:  A subset of 120 participants who received GAHT were compared to 246 participants who had not yet initiated treatment. Additionally, 65 participants who underwent top surgery following GAHT were compared to 134 participants who received GAHT only.Exposure: Data on GAHT and top surgeries were obtained from the National Prescribed Drugs Register, the National Patient Register and supplemented by self-reported survey data.Main outcomes and measures: GI, GD, and body satisfaction were assessed using the Transgender Congruence Scale, Gender Congruence and Life Satisfaction Scale, and Body Image Scale, supplemented by Visual Analogue Scale ratings at baseline and  up to three years post-treatment. We used linear mixed models (LMMs) within a Bayesian estimation framework, with time modeled as a natural cubic spline, retaining all longitudinal outcome data to account for within-person variation.Results: In the GAHT cohort, 67 (56%) among the treated were assigned female at birth, and 59 (49%) exhibited autistic traits. Among those undergoing top surgery, 57 (88%) were assigned female at birth, and 34 (52%) had autistic traits. Posterior estimates from the LMM supported the hypothesis that GAHT yields credible reductions in GI up to 31 months post-treatment, with delayed but credible improvements in GD and body satisfaction, though with increasing uncertainty over time. Top surgery was associated with sustained reductions in GI and early credible improvements in GD and body satisfaction, although posterior uncertainty increased in later follow-up periods. No significant interactions were found between GAHT or top surgery and autistic traits or autism diagnosis for any of the outcomes.Conclusion and relevance: GAHT is associated with improvements in core outcomes, particularly regarding GI, with further benefits following top surgery. No evidence was found to indicate that autistic traits or an autism diagnosis significantly moderate these associations. These results do not support the need for separate guidelines for access to gender-affirming interventions based solely on ASD status.