Background: The impact of the COVID-19 on the well-being of people with intellectual disabilities (PID) has been little studied. Methods: We analyzed its impact with a cohort study quantitatively analyzing anxiety, depression, organic symptoms, quality of life, and support needs in 24 PID, aged 19–74 years (x¯ 40, σ = 13.09), living in a residential center, before, during, and after the pandemic. Results: Their mental health improved unexpectedly at the onset of the lockdown although there was an increase in organic symptoms. But, with the progress of the lockdown, their mental health deteriorated drastically. On the contrary, as expected, their quality of life and support needs worsened from the beginning of the lockdown until the country returned to normality, a time when there was a general recovery, without reaching pre-pandemic levels. These results show that the mental health of PID was affected differently to that of people without intellectual disabilities.