Zoonotic influenza A viruses (zIAV) originating from avian and swine reservoirs present a serious concern for public health. Since the emergence of zIAV A(H5N1) in 1996, the virus has spread globally, impacting wild birds, poultry, wild and domestic mammals, including cattle and pigs, and sporadically infecting humans. Challenges persist in detecting and characterising zIAV, particularly at the human–animal interface. Recent external quality assessments conducted in the Netherlands and at European level have evaluated the capacity of human clinical diagnostic and national reference laboratories to detect, subtype and characterise potential zIAV. Based on these results, we reflect on the status and challenges of methods used for identifying cases of zIAV infection in Europe. While all laboratories are largely successful in generic detection of influenza A virus, subtyping is not widely used in clinical diagnostic laboratories. For national reference laboratories, subtyping specifically of swine-origin viruses remains challenging, often requiring sequencing for accurate identification. Although sequencing offers greater potential for characterising zIAV, training in the appropriate use of bioinformatics tools is needed. Raising awareness among healthcare professionals to document animal exposure in patient disease histories is also critical, as early suspicion of zoonotic infections is needed to direct laboratory testing, including subtyping.