A cogeneration system having flexible and controllable cogeneration loops. There is a first cogeneration loop to recover heat from a fuel cell power module, thereby producing a heat to electricity ratio between 0 and approximately 1.0. There is a second cogeneration loop to produce supplemental thermal energy for hot water generation and/or space heating. This loop can be connected or disconnected via switching valves depending on the thermal demands of hot water and/or space heating. This loop can also be useful to control the fuel processor temperature to prevent it from being overheated in cases when the fuel cell has low fuel utilization efficiency. With this second loop, it becomes possible to adjust the heat to electricity ratio at any desirable levels such as more than 2. It is also possible to produce the hot water at a higher temperature or superheated steam, which would have been difficult if only the first loop is used.