Subsyndromal delirium (SSD) in the Intensive Care Unit (ICU) is associated with an increased morbidity with unknown post-discharge functional and cognitive outcomes. We performed a prospective multicenter study to analyze the mental status of patients during their first 72 h after ICU admission and its trajectory, with follow-ups at 3 and 6 months after hospital discharge. Amongst the 106 included patients, SSD occurred in 24.5% (n = 26) and was associated with the duration of mechanical ventilation (p = 0.003) and the length of the ICU stay (p = 0.002). After the initial 72 h, most of the SSD patients (30.8%) improved and no longer had SSD; 19.2% continued to experience SSD and one patient (3.8%) progressed to delirium. The post-hospital discharge survival rate for the SSD patients was 100% at 3 months and 87.5% at 6 months. At admission, 96.2% of the SSD patients were fully independent in daily living activities, 66.7% at 3-month follow-up, and 100% at 6-month follow-up. Most SSD patients demonstrated a cognitive decline from admission to 3-month follow-up and improved at 6 months (IQCODE-SF: admission 3.13, p < 0.001; 3 months 3.41, p = 0.019; 6 months 3.19, p = 0.194). We concluded that early SSD is associated with worse outcomes, mainly a transitory cognitive decline after hospital discharge at 3 months, with an improvement at 6 months. This highlights the need to prevent and identify this condition during ICU stays.