The COVID-19 pandemic brought new challenges to the global community, reinforcing the role of public health in society. The main measures to combat it had (and still have) a huge impact on the daily lives of citizens. This investigation aimed to identify and monitor the population’s perceptions about how it faced this period and the impact on health, well-being, and daily life. In this study, we describe the main trends observed throughout the COVID-19 pandemic in terms of mental health status, confidence in the capacity of the health services to respond to the pandemic, and the use of health services by participants. The online survey collected responses from 171,947 individuals ≥16 years of age in Portugal, over a period of 15 weeks that started on 21 March 2020. Participants could fill the questionnaire once or weekly, which enabled us to analyse trends and variations in responses. Overall, 81% of the respondents reported having felt agitated, anxious, or sad during the COVID-19 pandemic; 19% did not experience these feelings. During the confinement period, the proportion of participants feeling agitated, anxious, or sad every day/almost every day ranged between 20 and 30%, but since the deconfinement this proportion decreased. Around 30% reported having more difficulty getting to sleep or to sleep all night; 28.4% felt more agitated; 25.5% felt sadder, discouraged, or cried more easily; and 24.7% felt unable to do everything they had to do, women more frequently than men. Overall, 65.8% of the participants reported feeling confident or very confident in the health services’ capacity to respond to the challenges associated with the pandemic, and this confidence increased over time. Concerning the people who needed a consultation, 35.6% had one in person and 20.8% had one remotely, but almost 44% did not have one due to cancellation by the service (27.2%) or their own decision not to go (16.3%). At this unusual time in which we find ourselves and based on our findings, it is essential to continue monitoring how the population is facing the different phases of the pandemic until it officially ends. Analysing the effects of the pandemic from the point of view of citizens allows for anticipating critical trends and can contribute to preventative action.