This study was conducted in response to the increasing prevalence of Alzheimer’s disease (AD) dementia and the significant risk faced by individuals with amnestic mild cognitive impairment with multiple-domain deficits (aMCI-md). Given the promising effects of MTPs, the primary aim of this study was to further explore their impact by assessing the maintenance of their benefits. Thus, 45 participants were randomly allocated in two groups: the Experimental group (n = 22), which received the metacognitive training program (MTP), and the Control group (n = 23) that received the cognitive exercises program (CEP). The training programs—the MTP and the CEP—included 10 individual sessions of a one-hour duration and took place once per week. To test the efficacy of the MTP, cognitive and metacognitive outcomes were compared between two groups—Experimental (EG) and Control (CG)—at four distinct time points: before–after–3 months–6 months after intervention. Based on this study’s findings, the positive effects of the MTP were evident over a six-month period. Specifically, already three months post-training, the CG began to show a decline in training-related gains. In contrast, the EG’s performance consistently improved, highlighting the superior efficacy of the MTP. Gains attributed to the MTP were detected in cognitive measures: cognitive flexibility and immediate visual recall, as well as in metacognitive measures: metacognitive control, improved metacognitive beliefs of attention, and an increased use of cognitive strategies. In conclusion, the results demonstrated the sustained effects of the MTP in cognitive and metacognitive measures over a period of six months, providing novel insight into the application and efficacy of the MTP in individuals with MCI.