It is well established that negative emotions influence a range of cognitive processes. How these emotions influence the metacognitive judgement individuals make about their own performance and whether this influence is similar depending on the conditions under which metacognition is assessed, however, is far less understood. The primary aim of this study was to determine whether exposure to emotional stimuli could influence metacognitive judgements made under short or long time constraints. A total sample of 144 young adults (aged 18–35 years) was recruited and asked to complete an arithmetic strategy selection task under emotional or neutral condition. Following each strategy selection trial, participants also provided a retrospective confidence judgement (RCJ). Both strategy selection and RCJ were collected under short or long time constraints (1,500 vs. 2,500 ms for strategy selection and 800 vs. 1,500 ms for RCJ). In addition to replicating previous findings showing lower rates of better strategy selection under negative emotions compared with neutral condition, an effect of negative stimuli on the accuracy of participants’ confidence judgements was found, but only if participants had a short time limit to make their second-level evaluation. Such findings are consistent with the hypothesis that exposure to emotional stimuli disturbs early, but not late metacognitive processes and have important implications to further our understanding of the role of emotions on metacognition.