In this study, conventional and organic olive tree nurseries were compared through a Life Cycle Assessment (LCA) analysis to identify processes that have a greater environmental impact and which of the two systems leads to lower greenhouse gas (GHG) emissions. Carbon sequestration in the woody biomass of the plants grown with both management systems was also considered. The research was carried out on six olive tree nurseries, four conventional and two managed also with an organic system, located in the nursery district of Pescia (Tuscany, Italy). The functional unit considered was two-year-old pot-grown plants (pot 15 cm Ø) and the results were expressed in terms of kg of CO2 equivalent (CO2eq). In all the nurseries analyzed, LCA showed that pots were the highest CO2eq emission source (45–63%), followed by potting mix (22.6–32.1%). This was due to the use of plastic in pots and peat for the growing media. Organic management was found to have a definite positive influence on the decrease of GHG, reducing the emissions up to 13% compared with conventional nurseries. Considering carbon stocked in the woody tissues of seedlings, the reduction of emissions attained 15.7% though a slightly lower (−6.7%) amount of CO2 incorporated into biomass was detected in the olive plants grown in organic nurseries. In light of our results, conversion of the nursery industry from conventional to organic management has the potential to reduce its carbon footprint.