Romania is currently facing many difficulties in order to cope with financial and economic crisis as well as to reach the Europe 2020 targets. This paper presents the new challenges faced by Romanian Research, Development and Innovation (RDI) system during the economic recession, its weaknesses and barriers that have hindered the implementation of the R&D structural reforms and delineate some benchmarks for overcoming them. Based on the most recent data and information about the Romanian RDI system, it attempted a qualitative analysis of the main aspects that may delay or stall its effective integration within European Research Area and may diminishing the R&D contribution to a quickly economic recovery. Ignoring the challenges confronting the Romanian research and innovation system, neglecting them in the prioritization of public funds allotment and overlooking effective incentives for increasing the private sector contribution to the RDI funding will keep labeling Romania as “modest innovator”, ranking it among the least in the EU regarding the performance indicators of the field.