Cheese whey (CW) is the main by-product of the dairy industry and is often considered one of the main agro-industrial biowaste streams to handle, especially within the European Union, where the diary activities play an essential role in the agrarian economy. In the paper, Life Cycle Assessment (LCA) is used to analyse the feasibility of producing polyhydroxyalkanoates (PHA) as the main output of an innovative CW valorisation route which is benchmarked against a conventional anaerobic digestion (AD) process. To this aim, the LCA inventory data are derived from lab-scale PHA accumulation tests performed on real CW, while data from the literature of concern are used for modelling both the PHA extraction from the accumulating biomass and for the alternative CW valorisation through AD. The comparison shows that AD would have better environmental performances than the baseline PHA production scenario. For example, the climate change indicator values result 44.8 and -35.7 kg CO2 eq./t CW for the baseline PHA recovery and AD, respectively. LCA proved to be a useful tool to highlight the weak points of innovative processes and suggest proper improvements. Once improved and again analysed through the LCA, the PHA production process from CW shows that environmental performance comparable to AD may be achieved. With reference, again, to the climate change indicator the value can be reduced to -50.3 kg CO2 eq./t CW for the improved PHA production process.