Abstract Uncertainty is a common and critical problem for planning the capacity and operation of integrated energy systems (IESs). This study evaluates the effects of uncertainties on the capacity and operation of an IES. To this aim, system planning and operation with uncertainties are optimized by a two-stage stochastic programming model and compared with a referencing deterministic case. Specifically, the uncertainties of photovoltaic (PV) generation and energy demand are investigated. Regarding system capacity, a larger energy storage capacity is needed to accommodate a higher uncertainty. The superimposed uncertainties have a higher effect on system capacity than the sum of the effect of each uncertainty. The uncertainty of energy demand has a higher impact than the uncertainty of PV generation. Regarding system operation, the increase in operation cost is smaller than the increase in investment cost and total cost. In addition, the average flexibility provided by the energy storage increases with uncertainty and uncertainties affect the change rate for power charging/discharging of the electric energy storage. Regarding the effect on the grid, the uncertainties increase not only the magnitude of ramping-rate, but also the frequency of power-dispatch.