The prebiotics like FOS and GOS are receiving special at-tention in the food industry due to their potential health benefits. They can be produced by enzymatic synthesis by using disaccharides or other substrates as raw materials or by extraction and hydrolysis from different natural sources (roots, legumes). However the environmental footprints of these different production schemes are lacking. This dataset presents Life Cycle Assessment (LCA) of the production of FOS and GOS by enzymatic synthesis from glucose (to get FOS) or lactose (to get GOS) and hydrolytic production from extraction of yacon potato (to get FOS) or chickpea (to get GOS). A cradle-to-gate approach was considered in the two scenarios under assessment (the phases of use and/or final disposal of FOS/GOS were not considered). The functional unit was defined as 100 g of FOS/GOS produced. LCAs were performed using data collected at the laboratory scale dur-ing experiments, supplemented with data from technical and scientific literature. Ecoinvent database provided background data. SimaPro was used for the LCA modeling with the mid-point impact EF2.0 characterization method to calculate en-vironmental impacts. For each scenario (FOS produced by synthesis, FOS produced by hydrolysis, GOS produced by syn-thesis, GOS produced by hydrolysis), the Life Cycle Inventory (LCI) and the Life Cycle Impact Assessment (LCIA) are pro-vided. These data can be used (i) to identify the main envi-ronmental hotspots of the production process, (ii) to compare the different process alternatives between them and (ii) to suggest eco-design options to upscale these processes. They could also be re-used in other LCA studies which would in-clude FOS and/or GOS in the production system.