The prevailing narrative about sexual declines during the transition to parenthood is largely based on studies assessing the average couple, but there is increasing evidence of variability in the sexual well-being of new parents. We sought to establish distinct subgroups of couples based on sexual function and sexual distress trajectories and examine biopsychosocial risk and protective factors of these trajectories. A prospective cohort of 257 first-time parent couples reported on sexual function and sexual distress from 20-week pregnancy (baseline) to 6 months postpartum across four time-points. Biopsychosocial factors were assessed at baseline and 3 months postpartum. Dyadic latent class growth analysis identified two distinct sexual function classes (high, 85%; discrepant, 15%) and three sexual distress classes (low, 77%; moderate, 12%; discrepant, 11%). We identified biomedical (vaginal delivery, perineal tear, breastfeeding) and psychosocial (fatigue, stress, anxiety, depression, attitudes toward sex during pregnancy, relationship quality, perceived partner support) factors that can be assessed at critical time-points (i.e., 20-week pregnancy and 3 months postpartum) to identify high-risk couples. Current results indicate that the course of change in sexual well-being for new parents is heterogeneous, with most new parents retaining high function and low distress and only a minority showing trajectories in which mothers, but not fathers, experience clinically significant and persistent levels of low sexual function and high sexual distress. These results may facilitate more nuanced approaches to the assessment and intervention of new parents’ sexual well-being.