Much remains unknown about compositional variations in soluble microbial products (SMP) with the shift of the substrate condition from a feast to a famine phase in biological treatment systems. This study demonstrated that the formation of SMP could be suppressed by up to 75% during the famine phase with the addition of essential nutrients. In contrast, presence of electron acceptor did not play any significant role during the stress condition, showing the similar amounts of SMP (r = 0.98, p < 0.05) formation between the bioreactors supplied with air and N. The SMP formed in the famine phase was more bio-refractory in the famine versus the feast phase with a linear correlation shown between the production and their aromatic structures in the composition (R > 0.95). The fluorescence excitation-emission matrix coupled with parallel factor analysis (EEM-PARAFAC) revealed the presence of four different fluorescent components, including two protein-like (C1 and C4), fulvic-like (C2), and humic-like (C3) components, in the SMP and bEPS formed at different conditions. Both C1 and C4 showed increasing trends (R > 0.95) with the length of starvation in the bioreactors without essential nutrients. Nutrient availability was found to be a key factor to quench the production of large-sized biopolymers. This study provides a wealth of information on operation conditions of activated sludge treatment systems to minimize large sized SMP molecules (particularly proteins), which typically exert many environmental concerns to effluent organic matter quality.