The ultimate fate of the degraded pollutants in biofiltration is not understood conclusively. Simple hydrocarbons such as toluene are often assumed to be completely mineralized to carbon dioxide especially in systems without supplemental nutrient addition. However many reports indicate this is not correct. The key focus of this work was to explicitly track and quantify toluene degradation to various carbon end-points and product ratios using soil as the active biofiltration matrix. Each carbon end-point was measured independently, as compared to determining one by difference, using gas chromatography and total carbon analysis of the solid and liquid phases. A differential biofiltration system was used which exposes the biofilm to uniform set of conditions at any given point in time. This allows interpreting the parameter driven response of the system in a more precise way as opposed to conventional biofilters where conditions change in space and time. The system was operated as a non-growth system to track the degraded carbon components in various phases. The average carbon balance closure was quantified to 90 % {85; 95} at (α=0.05) level of significance over 16 separate biofiltration experiments. Considering the experimental uncertainties and a robust statistical approach to propagating error estimates associated with combining independent sources, all the carbon can be considered to have been accounted for. The carbon endpoints were tracked as CO2 in the gas phase and the non-mineralized fractions cumulatively accumulated within the solid and liquid fractions of the system. The variation in CO2 recovery versus the non-mineralized fractions as a function of multiple environmental parameters was further investigated to elucidate the driving phenomena for the variations in carbon end-points. A factorial design approach was used to explore potential interactions and the main effects between three critical parameters (temperature, matric potential and substrate concentration) over a wide range chosen as categorical factors. A 3x3 factorial design matrix of temperature (20 °C, 30 °C, 40 °C) and toluene concentration (75 ppm, 120 ppm, 193 ppm) evaluated through a 2-way ANOVA indicated significant interactions resulting in CO2 recovery from toluene degradation varying from 54-90%. These results showed that mineralization is not always coupled with temperature because at the higher toluene concentration of 193 ppm, CO2 recovery was not statistically different (p-value < 0.05) across the temperature range unlike at lower inlet feeds. A 2x3 factorial design matrix evaluating temperature (20 °C, 40 °C) and matric potentials (-10 cmH2O, -20 cmH2O, -100 cmH2O) illustrated the significant main effect between the parameters without any significant interaction. CO2 recovery decreased at 20 °C from 71% at -10 cmH2O to 35% at -100 cmH2O. The corresponding elimination capacity of the system was influenced by significant interaction between all the studied parameters. Operations at 40 °C resulted in a 2-fold higher elimination capacities compared to 30 °C and 20 °C whereas elimination capacities decreased over operations at lower matric potentials. For operations at 40°C, elimination capacity decreased by almost ~30% with lower matric potential from -10 cmH20 to -100 cmH2O. Results from the start-up condition experiments with a lower initial feed concentration to subsequently higher feeds resulted in a two-three-fold increase in EC at the higher toluene concentration, compared to constant feeds starting at the higher concentration. An ECmax of 127 ± 2 g.m-3.h-1 was achieved going from 75-193 ppm feed before coming to a steady state EC of 38 ± 3 gm-3h-1. This can have significant practical implications in terms of acclimatization protocols. This experiment was investigated at 40 ᵒC and -10 cmH2O. The trends observed for CO2 recovery and EC, in particular start-up conditions, were also seen with the pure culture study with Pseudomonas putida. Microscopy work with lectin binding stain WGA-647 corroborated the findings of carbon end-points as the fate of non-mineralized carbon accumulating as EPS and other storage polymers. To summarize, this multivariable investigation into the fate of carbon end-points associated with toluene degradation provided potential insight on the impact on metabolic pathways and community structure from the quantified carbon fractions. However future work will be required to determine the relative importance of these two potential causes for shifting ratios of carbon endpoints. These results also provided a good framework to help bridge the connection between achieving better process efficacy through knowledge pertaining to the physiological response. This can be beneficial in deciding operational parameters, especially in regards to averting practical problems such as clogging and degradation stability.