There is a global need to create an environmentally low-impact and socially fair international food and agriculture system. Specifically, in the case of chocolate, since it is difficult to produce locally in consumer countries, the socio-economic impact and benefits of its production have long been unfairly distributed. This research analyses the differences between the global environmental impacts of Fairtrade-certified and organically produced cocoa (from Peru), sold in the form of a chocolate bar purchased in the Basque Country (Europe), and the respective average conventional product made with non-organic cocoa beans (from Ivory Coast). Life-cycle assessment (LCA) methodology was used to calculate five impact categories, while ReCiPe 2016 Midpoint Hierarchist was used to analyse the global warming potential (GWP), terrestrial ecotoxicity (TE), and environmental footprint (ENVF, for land use); AWARE was used to measure the water footprint (WF); and cumulative energy demand (CED) assessed energy footprint (EF). The selected functional unit (FU) is 1 kg of final chocolate bar (72% cocoa), extrapolating the characteristics of a 150 g bar. The system boundaries take into account a cradle-to-gate LCA covering the following phases: the production of ingredients, the processing of cocoa paste, transportation and packaging, the manufacture of the chocolate, and its final retail distribution. The results show that certified Organic Agriculture and Fairtrade (OA&FT) chocolate had an average global warming potential (GWP) of 3.37 kg CO2-eq per kilogram, 57.3% lower than Conventional Agriculture (CA)-based chocolate, with the greatest reduction associated with the production of ingredients, at −71.8%. The OA&FT chocolate studied had an 87.4% lower impact in the category of terrestrial ecotoxicity (TE) than that of the CA-based chocolate, yielding 13.7 and 108.6 kg 1,4-DCB per kilogram, respectively. The greatest reduction in the TE impact category also occurred for the OA&FT chocolate in the ingredient production phase, at 93%. Reductions in energy footprint (EF) and water footprint (WF) were also observed in the OA&FT product (21% and 5%). In contrast, although OA&FT processing drastically reduced the associated environmental loads, an increase in packaging and transport phase impacts was observed in the GWP and TE categories (95% and 107%, respectively). Similarly, an increase of 18.7% was observed in the land use footprint for the OA&FT chocolate. The greater need for cropland is compensated by the reduction of 449.02 kg 1,4-DCB·person−1 year−1 in the TE category. This research shows that replacing the current consumption of CA cocoa with OA&FT cocoa has the potential to reduce the GWP by 21.95 kg CO2-eq·person−1·year−1, reducing the current Basque average emission range of 8.4 tCO2-eq·yr−1 by 0.26%. As a future subject to study, it was also found that the impact of long-distance maritime transportation and packaging could still have the potential to be reduced, it currently being the cause of up to 11% of the GWP from OA&FT cocoa.