Aquaculture is globally the fastest growing sector of agriculture that needs to be sustainable and must also meet bioeconomic demands. In principle, aquaponics, the combination of aquaculture and horticulture within a single recirculating aquaponic system (SRAPS), provides a sustainable approach; however, it has lower productivity of both fish and plants in comparison to separate recirculating systems. The aim of our new concept for aquaponics is to improve sustainability and productivity concomitant with lowering environmental emissions. The aquaponic system for (nearly) emission free tomato and fish production in greenhouses (ASTAF-PRO) is a new combination of systemic parts, consisting of 2 independent recirculating units: an aquaculture system (RAS) for fish and a hydroponic unit for plants. Both systems are connected by a 1-way valve to deliver fish water containing nutrients into the hydroponic reservoir, where the fish water can be optimized as fertilizer in order to meet specific demands of the plant species. Thus, our double recirculation aquaponic system (DRAPS) can provide optimum conditions for both parts to increase productivity and to prevent any adverse interactions between plant and fish units. Water use is minimized by condensing the plant evapo-transpired water via air conditioning and returning it into the RAS. Testing of the ASTAF-PRO prototype successfully demonstrated the principle using a combination of tilapia and tomato production. Tilapia productivity was similar to single RAS, while tomato production at least indicated the potential for similar efficiency to conventional hydroponics. Thus, ASTAF-PRO improves sustainability and productivity while lowering environmental emissions, and might promote future application of aquaponics for food security.