Cooperation for innovation, not only enhances the innovative and economic performance of companies but also fosters growth and strengthens the resilience of firms in the realm of innovation activities. In this study, we delve into the cooperative activities of innovative Spanish companies with their European counterparts. We employ six logit models using panel data to scrutinize the impact of ownership on innovation cooperation and the determinants of collaboration across different phases of the business cycle, spanning from 2004 to 2016, which we divide into three sub-periods: the pre-crisis (2004–2007), the crisis (2008–2013), and the recovery (2014–2016). Throughout the businesses cycle, state-owned enterprises are the most prone to engage in cooperative innovation with European partners, while unaffiliated domestic firms are the least prone. Foreign subsidiaries clearly outperform unaffiliated domestic firms and slightly outperform domestic business groups in prosperous times, but do not outperform state-owned enterprises even during crises. The drivers of cooperation for innovation with European partners evolve over time, becoming particularly challenging during crises. The factors influencing cooperation with European universities exhibit distinct characteristics. The results contain policy and management implications.