The following article is focused on the issues of development of innovative economy based on statistics and sythesis of previously conducted scientific researches. These challenges are analysed through the case study of Germany and Spain as they represent different groups of countries in terms of innovation and feature various approaches to overcome the problems.Such problems as: inability to adapt to the objective trend to slow down the widespread introduction of innovations, underfunding of high-tech industries, lack of radical innovations, narrow scope of higher education specializations, lack of mechanisms to protect investors in innovative projects and inconsistency of legislation regulating innovative activity are considered typical for Germany. The issues of underestimation of the innovative potential of the state, lack of infrastructure and coordination between its facilities, high level of bureaucracy, insufficient training and inefficient use of resources are the ones that Spainish economy faces. Detection of the above listed challenges allows to develop recommendations to resolve the issues of German and Spanish innovative economics. Their expirience would to be useful in identifying the challenges of the current situation and in formulating development strategies for states with similar problems, including Russia.