Naturally occurring materials such as jute and coir have some favorable engineering characteristics and also degrade over time, so they have increasingly been used in engineering applications in recent years. The efficient way that naturally prefabricated vertical drains made from those materials help accelerate soil consolidation has been shown in previous studies, but they also tend to decompose rapidly in adverse environments, where cellulose-degrading bacteria cause a serious deterioration of their favorable drainage properties. This study presents a laboratory investigation into the biodegradation of prefabricated vertical jute drains in saturated soft soils, where the tensile strength of jute and coir fibers and the discharge capacity of drains decrease in response to different environments. Micro-observation also shows a transformation of the jute fibers and destruction of the drain structure due to biodegradation. DNA extraction and sequencing techniques to determine the microbial properties of these decayed fibers indicate that bacteria such as species of the genera Clostridium and Bacillus can cause rapid decomposition of cellulose-based material (i.e., jute), whereas other organic matter-consuming microbes such as sulfate-reducing bacteria do not directly contribute to the biodegradation of jute. In response, an analytical approach that incorporates various forms of drain discharge capacity over time is proposed to predict soil consolidation. The results indicate there is considerable deviation in dissipating the excess pore pressure when the drain degrades in different ways.