Medium chain length (mcl) polyhydroxyalkanoate (PHA) polymers were produced by Pseudomonas putida LS46 from the hydrolysed long-chain fatty acids (LCFAs) of vegetable oils. LCFAs are sustainable and economical substrates for mcl-PHA production which get converted into mcl-PHAs from the microbial fatty acid degradation pathway. As such, good polymer yields have been obtained from fatty acids and their functional groups can be retained in the polymer. The length and degree of unsaturation in the substrate is correlated to the polymer composition. The comparison of mcl-PHA synthesis using octanoic acid or LCFAs of P. putida LS46 in response to microaerophilic conditions differs based on substrate. Grown on octanoic acid, cell division ceased under microaerophilic conditions with carbon flux towards mcl-PHA accumulation. In contrast, growth continued on LCFAs at a linear rate consistent with the growth rate at onset of limitation (0.36 g L-1 h-1) but mcl-PHA accumulation also began to increase. This work demonstrated the differential biochemical response in microaerophilic conditions of P. putida LS46 and indicated that feeding strategies could be designed to improve productivity, tailor polymer properties and reduce production costs. The polymer properties of mcl-PHAs produced using varied carbon substrates were analysed to determine the effect of substrate biochemistry on monomer composition and crystallinity. Significant variations in monomer composition and molecular weights were observed based on substrate, and whether de novo fatty acid synthesis or fatty acid degradation pathways were necessary for metabolism. A relationship between monomer composition and mechanical and thermal properties was observed and reported. Due to the absent crystallinity of mcl-PHAs from unsaturated substrates, alternative applications involving the functionalization from these moieties are required for mcl-PHAs from many LCFAs. We hypothesized that oxidative cleavage of the unsaturated mcl-PHA side chains would reintroduce crystallinity. Ozonolysis and osmium-tetroxide catalysed olefin cleavage were investigated and resulted in limited residual unsaturation and higher purity is achieved as contaminant fatty acids are further removed. Resulting polymer observations and secondary oxidation are reported herein.