Caffeine, a widely found component in food and pharmaceuticals, is harmful to ecosystem when discharged into the environment because of its non-eco-friendly nature and recalcitrant properties. Complete caffeine degradation by methanogenesis was successful for the first time in a man-made bioreactor. We confirmed the success through continuously operating a bioreactor, testing the methane potential and determining the kinetic behaviour. In the continuous operation, an 87.5 +/- 5.3% removal efficiency of caffeine was observed using an anaerobic membrane bioreactor for the digestion of coffee processing wastewater in the long-term process. In methane potential tests with caffeine as the sole substrate, the complete conversion from caffeine to CH4 was achieved in a caffeine-rich environment with a caffeine concentration up to 2000 mg/L. We have proposed and confirmed a reaction equation for the caffeine degradation by methanogenesis based on the stoichiometric relationship between the degraded caffeine and the increased end-products: CH4, NH4+-N and CO2. In the kinetic behaviour experiment, the regular monitoring the residual caffeine and the end-products indicated that methanogenic degradation of caffeine clearly includes two major steps: caffeine converting to intermediates and the intermediates converting to CH4. The major accumulated intermediates should be hydrolysis products and the process of hydrolysis products converting to volatile fatty acids was identified to be the rate-limiting step of caffeine degradation. This work provided a new thought to microbial caffeine degradation and will be useful in developing innovative technology for bioenergy harvest at the same time of decaffeination.