Although cross-sectional studies show heterogeneity in emotional cognition in bipolar disorder (BD), the temporal course within subgroups is unclear. In this prospective, longitudinal study we assessed the trajectories of emotional cognition subgroups within a 16-month follow-up period in recently diagnosed BD patients compared to healthy controls (HC). Recently diagnosed BD patients and HC underwent comprehensive emotional and non-emotional testing at baseline and again at follow-up. We employed hierarchical cluster analysis at baseline to identify homogenous emotional cognition subgroups of patients, and changes across the subgroups of BD and HC were assessed with linear mixed-model analyses. We found two emotional cognition subgroups: subgroup 1 (65%, n = 179), showing heightened negative emotional reactivity in neutral and negative social scenarios and faster recognition of emotional facial expressions than HC (ps<0.001, n = 190), and subgroup 2 (35%, n = 96) showing blunted reactivity in positive social scenarios, impaired emotion regulation, poorer recognition of positive and slower recognition of all facial expressions than HC (ps≤.03). Subgroup 1 exhibited normalization of the initial emotional cognition abnormalities in follow-up. In contrast, subgroup 2 showed a lack of improvement in reactivity positively-valenced emotional information. Patients in subgroup 2 presented more and longer mixed episodes during the follow-up time and were more often prescribed lithium. One third of patients display blunted emotional reactivity, impaired emotion regulation abilities and facial expression recognition difficulties also show persistent impairments and poorer course of illness. This subgroup may indicate a need for earlier and more targeted therapeutic interventions.