Mental health disparities among transgender and gender diverse (TGD) populations have been documented. However, few studies have assessed differences in mental health symptom severity, substance use behavior severity, and engagement in care across TGD subgroups. Using data from the electronic health record of a community health center specializing in sexual and gender minority health, we compared the (1) severity of self-reported depression, anxiety, alcohol use, and other substance use symptoms; (2) likelihood of meeting clinical thresholds for these disorders; and (3) number of behavioral health and substance use appointments attended among cisgender, transgender, and non-binary patients. Participants were 29,988 patients aged ≥18 who attended a medical appointment between 2015 and 2018. Depression symptom severity (F = 200.6, p < .001), anxiety symptom severity (F = 102.8, p < .001), alcohol use (F = 58.8, p < .001), and substance use (F = 49.6, p < .001) differed significantly by gender. Relative to cisgender and transgender individuals, non-binary individuals are at elevated risk for depression, anxiety, and substance use disorders. Gender was also associated with differences in the number of behavioral health (χ² = 51.5, p < .001) and substance use appointments (χ² = 39.3, p < .001) attended. Engagement in treatment among certain gender groups is poor; cisgender women and non-binary patients assigned male at birth were the least likely to have attended a behavioral health appointment, whereas transgender men and cisgender women had attended the lowest number of substance use appointments. These data demonstrate the importance of (1) assessing gender diversity and (2) addressing the barriers that prevent TGD patients from receiving affirming care.