The COVID-19 pandemic has an indirect impact on the health and welfare of animals. The aim of this work was to investigate the effect of COVID-19 on Municipal and Association animal shelters. A questionnaire was sent to 97 Municipal shelters and 65 Associations. Questions focused on public funding, management and animal welfare during COVID-19 restrictions. The response rate was 43.3% (42/97) for Municipal shelters and 38.5% (25/65) for Associations. Municipal shelters (67%) received over 80% of public funding, whereas 68% of the Associations received less than 50%. During the COVID-19 restrictions, financial difficulties were observed by 52% of Associations and 5% of Municipal shelters, and a lack of volunteers was observed by 56% of Associations and 17% of Municipal shelters. Operational difficulties were indicated by 43% of Associations and 12% of Municipal shelters, and a lack of instructions was observed by 31% of Municipal shelters and 4% of Associations. No significant differences were obtained on abandonment, adoption, clinical support, exercise and interaction. Decreased feed supply was reported by 40% of Associations and 5% of Municipal shelters. During the COVID-19 restrictions, Municipal shelters were more affected by the lack of instructions, and Associations were more affected by external factors such as a decrease in feed supply, volunteers and funding. Preparedness and contingency plans seem essential to face unpredicted crises.