The fact that SARS-CoV-2 has reportedly infected companion, livestock and wildlife animals may constitute a significant risk for virus reservoirs, ground for emerging variants and potential for novel reverse zoonosis. Hence, SARS-CoV-2 surveillance in animal species is crucial to prevent emerging variants which may spread to humans. The present study aimed to develop a simple, high-throughput and ultrafast magnetic bead immunoassay to detect anti-SARS-CoV-2 nucleocapsid and spike reactive IgG antibodies in dog and cat serum samples. The assays were validated using serum from eleven dogs and cats which had SARS-CoV-2 infections confirmed by real-time RT-PCR. The negative cohort consisted of pre-pandemic dog and cat samples. The assays performed at 73–82% sensitivity and 97.5–98% specificity for dogs and 71% sensitivity and 92–94% specificity for cats. The lower assay specificity for cats is explained by the fact that cat pre-pandemic sera showed high levels of cross-reactive with SARS-CoV-2 Nucleocapsid and Spike, supporting that these animals have been exposed to other coronavirus sharing structural similarities with SARS-CoV-2. These assays described in this work are now being used for SARS-CoV-2 surveillance and research purposes.