In this study we analysed the environmental and economic profile of current agricultural practices for greenhouse crops, in cold and warm climates in Europe, using four scenarios as reference systems: tomato crop in a plastic greenhouse in Spain, and in glasshouses in Hungary and the Netherlands, and rose crop in a glasshouse in the Netherlands. This study is in the context of the EUPHOROS project “Efficient Use of Inputs in Protected Horticulture”. The aim of EUPHOROS project is to improve horticultural production systems in Europe by developing cleaner production alternatives from both an environmental and economic point of view. The methodologies selected for the study were Life Cycle Assessment for the environmental analysis and cost-benefit analysis for the economic assessment. Dutch reference systems used a combined heat and power (CHP) system for the production of thermal energy and electricity. Two approaches were used to study the multifunctionality of CHP: system expansion and energy allocation. The main environmental burdens in the four scenarios were energy consumption, greenhouse structure and fertilizers. Environmental impacts due to energy consumption can be reduced by using co-generation or geothermal water in glasshouses. The structure contribution can be decreased with the improvement of recycled materials and design. Adjustment of fertilizer doses and closed irrigation systems are recommended in Spain and Hungary. The best economic perspectives to reduce inputs are energy savings in glasshouses and reduction of fertilizers in Spain and Hungary. The study shows the importance of including economic and environmental aspects in sustainability studies.