The COVID-19 pandemic has prompted countries to swiftly implement rigorous preventive measures on a population-wide scale worldwide. However, in low-income countries like Mozambique this was difficult, coupled with a generalised lack of knowledge on how the population understood and complied with these measures. This study assessed community perceptions and implementation of anti-COVID-19 measures recommended by Mozambican authorities in Manhiça and Quelimane districts, including confinement, social distancing, frequent handwashing, mask wearing, and quarantine as the key practices to evaluate. We conducted a cross-sectional quantitative survey in October 2020 and February 2021, interviewing heads of households, face-to-face. The data collected included self-evaluation of compliance and existence of handwashing facilities and face-masks in the households, aided by observations. We present descriptive statistics on perceptions and compliance at individual and household levels. Out of the 770 participants, nearly all (98.7%) were aware of Coronavirus disease, including the term COVID-19 (89.2%). Knowledge varied between districts, with Manhiça participants showing higher levels of sufficient ability to define the disease. The symptoms most mentioned were dry cough (17.8%), fever (15.7%), flu-like symptoms (14.2%), breathing difficulties (13.6%), and headache (13.1%). Participants recognized various transmission modes, including touching infected objects and inhaling infected air. Preventive measures like handwashing with soap or sanitizing hands with alcohol, wearing masks, and social distancing were acknowledged, but the understanding varied. Compliance with these measures was generally low, with fewer than half of respondents reporting adherence to them. Only 30.4% of households had handwashing facilities (of which only 41.0% had water), and masks were often limited to one per person aged 6 years or more. Community members in Manhica and Quelimane were aware of COVID-19 but had limited understanding of what the preventive measures meant, and had lower levels of compliance. Understanding and addressing the factors affecting the proper implementation of these measures is crucial for improving community adherence in preventing infectious diseases with epidemic potential.