The role of energy crops in reducing fossil energy use and greenhouse gas emission is much debated. To improve decision making on the use of crops for producing bioenergy, a tool (Energy Crop Simulation Model or E-CROP) has been developed to calculate 1) sustainable crop dry matter yield levels as function of agricultural inputs, and 2) gross and net energy yield and greenhouse gas emission reduction, covering the entire bioenergy production chain from sowing to distribution of bioenergy. E-CROP can be applied to a wide range of crops, soils, climatic conditions, management choices, and conversion technologies. This paper describes E-CROP and focuses on its application on four arable crops, as cultivated on two contrasting sites in the Netherlands (potato and sugar beet for bioethanol, winter oilseed rape for biodiesel and silage maize for bioelectricity) and on the effect of crop management (viz. irrigation and nitrogen fertilisation). In all situations, gross energy output exceeded total energy input. Calculated for an average situation, net energy yield ranged from 45 to 140 GJ·ha-1. Lowering irrigation and/or fertilisation input levels generally resulted in a reduction of net energy yields. The net reduction of greenhouse gas emissions in the average situation ranged from 0.60 to 6.5 t CO2-eq·ha-1. In general, N2O emission from nitrogen fertiliser caused large variations in the net reduction of greenhouse gas emission, which even became negative in some situations. Lowering nitrogen fertilisation to levels that are suboptimal for net energy yields enhanced the net reduction in greenhouse gas emission, implicating that both goals cannot be optimised simultaneously. Agricultural knowledge is important for optimising the outputs of bioenergy production chains.