There is an increased risk for depression and anxiety across the perinatal period (i.e., spanning pregnancy and the first year postpartum); however, limited research has examined elevations in core negative affectivity underlying internalizing disorders more broadly. The current study sought to characterize trajectories of core internalizing problems among both mothers and fathers across the perinatal period and explored whether modifiable risk and protective factors buffered risk for elevated symptoms during this key developmental transition. A community sample of mixed-sex couples ( = 159) completed assessments during pregnancy and at four postpartum timepoints. Using growth mixture modeling, we found that 21.2% of mothers demonstrated clinical elevations in core internalizing symptoms that persisted up to 2 years postpartum. In contrast, 7.8% of fathers demonstrated clinical elevations in core internalizing symptoms across this period, with an additional 29.0% of fathers demonstrating subthreshold symptom elevations. Concerns related to pregnancy and childbirth and paternal (partner) internalizing problems during pregnancy conferred risk for elevated symptoms in mothers, whereas psychological flexibility, emotional intimacy, and the quality of received support were identified as protective factors for fathers. Results highlight the importance of repeated screening for internalizing problems and suggest that promoting a strong interparental relationship is critical for emotional health and well-being across the perinatal period.