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, supplemented with data from Ecoinvent database. SimaPro was used for the LCA modeling with the midpoint impact EF2.0 characterization method. For each scenario (FOS produced by synthesis, FOS produced by hydrolysis, GOS produced by synthesis, GOS produced by hydrolysis), the Life Cycle Inventory (LCI) and the Life Cycle Impact Assessment (LCIA) are provided.