Flexible work arrangements, such as teleworking, have gained massive and unprecedented usage for creating work environments that foster well-being and productivity. Yet empirical evidence is still scant and not much is known about the role of organizational climate(s) in this process. Accordingly, the present study was set out to investigate the mediating mechanisms linking flexible teleworking to scientific productivity by considering climate for well-being dimensions, the climates for excellence and for innovation, and eudaemonic well-being as mediating constructs. Data were collected from 358 members of 48 Spanish European Research Council (ERC) granted teams and analyses were conducted both at the individual and team level, after checking for the relevant aggregation indexes. Relevant and significant relations were found within the hypothesized statistical model both at the individual and team level of analysis. The climate dimension of team support and the climate for innovation, together with eudaimonic well-being, resulted to be linked by significant relationships suggesting a potential mediating path. Also, empirical evidence supported considering gender as a control variable for the relationship between flexible teleworking and the climate dimension of work-life balance. In conclusion, climate variables and eudaimonic well-being represent relevant variables for the explanation of the relationship between flexible teleworking and scientific productivity. Practical and theoretical implications, and limitations are further discussed in the article.