Background: Bipolar disorder (BD) is associated with impairments in both emotional and non-emotional cognition. Recently, cognitive impairments have attracted increasing research interest as markers of prognosis and possible treatment targets in patients with BD. However, there is a paucity of studies investigating cognitive predictors of prognosis in BD. Methods: We assessed 148 recently diagnosed, symptomatically stable patients with BD with a battery of emotional and non-emotional cognitive tests and followed them up over 16 months as part of an ongoing cohort study. Multiple linear regression analyses were conducted to examine the associations between cognitive performance at baseline and the recurrence and duration of (hypo)manic and depressive episodes, respectively, with adjustment for age, sex, subsyndromal symptoms and time between assessments. Results: Poorer recognition of negative facial expressions and more negative emotions in neutral daily life scenarios were associated with greater frequency (ps ≤ .04) and longer duration (ps ≤ .03) of subsequent (hypo)manic episodes over the 16-month follow-up period. In addition, poorer global cognition, attention and psychomotor speed, and verbal fluency were associated with more (hypo)manic episodes (ps ≤ .04). Finally, more difficulty down-regulating emotion in negative social scenarios was associated with depressive relapse (p = .007). It was a limitation that patients had a delayed diagnosis of seven years from their first mood episode despite being recently diagnosed. Conclusion: Trait-related cognitive impairments influence the early course in recently diagnosed patients with BD, particularly (hypo)manic relapse. Early prophylactic strategies targeting cognitive impairments may increase resilience and the course of illness in recently diagnosed patients with BD.