Population growth has led to an increase in food production, resulting in an increase in agricultural products in terms of quantity and quality. Quinoa (Chenopodium quinoa Willd.) cultivation is prevalent in most areas of the world due to its high-quality grain and its potential to produce high yields under tough growing conditions. This study aimed to investigate all greenhouse gas (GHG) emissions generated by quinoa seed production in Greece and their relationship with farm-related factors, from fertilizer production to energy consumption for all cultivation techniques. The amount of all GHG emissions was estimated using Cool Farm Tool software. In order to collect data, a questionnaire including questions regarding cultivation details, soil characteristics, inputs, fuel, and water use was distributed and completed by forty quinoa producers from Central Greece. Accordingly, the estimated carbon footprint values per hectare and per kilogram of quinoa seed were 1,159.65 and 0.48 kg CO2-eq, respectively. The present research also found that the highest CO2-eq emissions per kilogram of quinoa seed were found to be associated with the production of fertilizers, with a value of 0.20 kg CO2-eq corresponding to 40.88% of the total emissions per kilogram of produced seed. Consequently, attention must be given for the mitigation of the environmental impact of quinoa seed production. It is particularly important to manage chemical fertilizers and agricultural machinery properly in order to ensure the sustainable cultivation of quinoa.