Codigesting fats, oils, and greases with municipal wastewater sludge can greatly improve biomethane recovery at wastewater treatment facilities. Process loading rates of fats, oils, and greases have been previously tested with little knowledge of the digester microbial community structure, and high transient fat loadings have led to long chain fatty acid (LCFA) accumulation and digester upsets. This study utilized recently-developed quantitative PCR assays for syntrophic LCFA-degrading bacteria along with 16S amplicon sequencing to relate changes in microbial community structure to LCFA accumulation during transient loading increases to an anaerobic codigester receiving waste restaurant oil and municipal wastewater sludge. The 16S rRNA gene concentration of the syntrophic β-oxidizing genus Syntrophomonas increased to ∼15% of the Bacteria community in the codigester, but stayed below 3% in the control digester that was fed only wastewater sludge. Methanosaeta and Methanospirillum were the dominant methanogenic genera enriched in the codigester, and together comprised over 80% of the Archaea community by the end of the experimental period. Constrained ordination showed that changes in the codigester Bacteria and Archaea community structures were related to measures of digester performance. Notably, the effluent LCFA concentration in the codigester was positively correlated to the specific loading rate of waste oil normalized to the Syntrophomonas 16S rRNA concentration. Specific loading rates of 0-1.5 × 10(-12) g VS oil/16S gene copies-day resulted in LCFA concentrations below 30 mg/g TS, whereas LCFA accumulated up to 104 mg/g TS at higher transient loading rates. Based on the community-dependent loading limitations found, enhanced biomethane production from high loadings of fats, oils and greases can be achieved by promoting a higher biomass of slow-growing syntrophic consortia, such as with longer digester solids retention times. This work also demonstrates the potential for controlling the loading rate of fats, oils, and greases based on the analysis of the codigester community structure, such as with quantitative PCR measurements of syntrophic LCFA-degrading bacteria abundance.