The non-structural protein 1 (A/NS1) of influenza A viruses (IAV) harbours several src-homology domain (SH) binding motifs that are required for interaction with cellular proteins. The SH3 binding motif at aa212-217 [PPLPPK] of A/NS1 was shown to be essential for binding to the cellular adaptor proteins CRK and CRKL. Both regulate diverse cellular effector pathways, including activation of the MAP-kinase JNK that in turn mediates antiviral responses to IAV infection. By studying functional consequences of A/NS1–CRK interaction we show here that A/NS1 binding to CRK contributes to suppression of the antiviral-acting JNK–ATF2 pathway. However, only IAV that encode an A/NS1-protein harbouring the CRK/CRKL SH3 binding motif PPLPPK were attenuated upon downregulation of CRKI/II and CRKL, but not of CRKII alone. The PPLPPK site-harbouring candidate strains could be discriminated from other strains by a pronounced viral activation of the JNK–ATF2 signalling module that was even further boosted upon knock-down of CRKI/II. Interestingly, this enhanced JNK activation did not alter type-I IFN-expression, but rather resulted in increased levels of virus-induced cell death. Our results imply that binding capacity of A/NS1 to CRK/CRKL has evolved in virus strains that over-induce the antiviral acting JNK–ATF2 signalling module and helps to suppress the detrimental apoptosis promoting action of this pathway.