Transgender people and their next-of-kin may request information on sexual orientation and preferred partners during hormonal affirming process. Although previous research on sexual orientation in transgender people is extensive, this literature may already be outdated and/or the methodology of studies assessing sexual orientation may fall short. This prospective cohort study was part of the European Network for the Investigation of Gender Incongruence (ENIGI). Gender role and preferred partner in sexual fantasies, sexual orientation and gender of current sexual partner were assessed at baseline (initiation of HT) and every follow-up visit. Data from 469 transgender women (TW) and 433 transgender men (TM) were analyzed cross-sectionally and prospectively. At baseline, more than half reported having no partner (35% of TW, 47% of TM). After 12 months, more than half reported having a partner (59% of TW, 56% of TM), with no changes between one and three years of HT. The majority of TM preferred a female partner, TW preferred male and female partners. The sexual identity of their partner matched their sexual orientation in >80%. Sexual orientation did not change over time. We did not observe associations with serum levels of sex steroids or gender-affirming surgery (chest or genital surgery). Sexual orientation did not change during hormonal transition and was not associated with sex steroids or surgery. Also, preferences matched the partner’s sexual identity. We do not assume that changing serum levels of sex steroids is directly associated with changes in partner choice. The number of people with a current partner increased, possibly due to the indirect effects of gender-affirming care.