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To develop innovation, firms make several decisions on the allocation of resources to specific innovation activities. Important innovation decisions include among others the decision to collaborate with other partners for innovation activities and the decision to engage in complex R&D projects such as projects with environmental benefits. Although there are very few empirical works that examine these two decisions together, while supporting that R&D collaborations are more important for the development of environmental innovations than for conventional innovations, an empirical work that examines the joint impact of these two decisions on corporate innovation efficiency is still lacking. This study aims to fulfill this gap by making one of the first attempts to employ a new dataset based on the Greek Community Innovation Survey (CIS), conducted for the years of 2012–2014 analyzing 2456 companies. Econometric results indicate that firm’s decision to eco-innovate exerts a positive influence on firms’ innovation efficiency directly. On the contrary, regarding the decision to engage in R&D collaborations, econometric results indicate that there is not a direct or an indirect, via eco-innovation, impact on innovation efficiency.