Phthalate esters (PAEs) are a group of endocrine-disrupting organic chemicals commonly used as additives in the manufacturing of a wide range of plastics. Large quantities of different phthalate esters have been used in specific products for quality and performance by the manufacturing industries, and they pose a significant risk to human health and the ecological quality of the environments due to leaching out of phthalates from plastic products and their high mobility. Since phthalate esters are most removed efficiently through biodegradation by microorganisms in the environments, it is important to understand the efficiency, microorganisms involved, biochemical transformation processes and mechanisms of phthalate metabolism by the specific microorganisms. This article addresses the degradation of endocrine-disrupting phthalates and their fates by an integrative comparison and analysis on efficient PAEs-degrading microorganisms, the microbial metabolism, and the biochemical processes and limitation. The comparison reveals that no significant difference is evident on efficiencies between single strains of bacteria or the mixed bacterial consortia when degradation can be carried out. However, there are a few important characteristics among the efficiencies of the PAEs-degrading bacteria. The microorganisms shall utilize the specific phthalate ester as the sole source of carbon and energy. They shall mineralize the substrates, including the original compound and its degradation intermediates to achieve a complete removal. In addition, it is of practical importance for the bacteria to adapt and survive in a range of temperatures, salinity and pH as well as in the presence of indigenous microorganisms in bioremediation of contaminated sites or wastewater treatment. This review also reveals that caution should be given to both the presentation and interpretation of the degradation results for a comprehensive knowledge, particularly data on bacterial growth, extraction and analysis of residual PAEs, and the confounding use of surfactants or co-substrate in the research. The public awareness of plasticizers as an environmental pollutant is mostly due to its increasing quantities being used, constant contacts with human population on a daily basis and potential health hazards. Its toxicity shall be address more focused on reproductive biology meaningfully than the traditional mortality test in toxicology for the significant effects on animals including human.