Anxiety and depressive disorders are characterized by high rates of recurrence, substantially contributing to the high burden associated with these disorders. It is therefore crucial to identify factors related to recurrence, as they may provide viable targets for preventative intervention. Previous studies have observed a link between low self-esteem and subsequent symptoms of depression and anxiety, and low levels of self-esteem in those recovered from a depression or an anxiety disorder. Research also suggests that it is crucial to differentiate more explicit self-esteem (ESE) from more implicit self-esteem (ISE). The current study is the first to test whether ISE and ESE predict recurrence of depression and recurrence of anxiety during a 3-year follow-up as determined with clinical interviews. The sample included those with a history of a depressive disorder (n = 559) and/or a history of an anxiety disorder (n = 458) who had been depression- and anxiety-free for at least six months at baseline. During the 3-year follow-up, 119 (21%) and 104 (23%) had a depression and anxiety recurrence, respectively. ISE predicted recurrence of both depression and anxiety, even when statistically controlling for residual symptoms and neuroticism at baseline. ESE also showed predictive value, although this was not over and above residual symptoms. Explorative analyses suggest that ESE and ISE improved little, or not at all, from currently having a depression or anxiety disorder to recovery. These results therefore suggest that ISE may be an important target for interventions to prevent the recurrence of both depression and anxiety disorders.