The great increase in livestock production in some European areas makes it necessary to recycle organic slurries and manures and to integrate them in crop production. In Northeast Spain, the application of pig slurry (PS) is being extended to alternative crops such as rice due to the great increase in pig production. However, there is a lack of information of the effect of substitution of synthetic fertilizers with pig slurry on greenhouse gas (GHG) emissions in rice crop, and this information is key for the sustainability of these agricultural systems. The aim of this study was to evaluate the effect of the substitution of mineral fertilizers by PS on GHG emissions in Mediterranean flooded rice cultivation conditions under optimal nitrogen (N) fertilization. Two field experiments were carried out in two different (contrasting) soil types with different land management. Site 1 had been cultivated for rice in the previous three years with no puddling practices. Site 2 had been cultivated for rice for more than 15 years with puddling tillage practices and had higher organic matter content than site 1. The cumulative nitrous oxide emissions during the crop season were negative at both sites, corroborating that under flooded conditions, methane is the main contributor to global warming potential rather than nitrous oxide. The substitution of mineral fertilizer with PS before seeding at the same N rate did not increase emissions in both sites. However, at site 1 (soil with lower organic matter content), the higher PS rate applied before seeding (170 kg N ha−1) increased methane emissions compared to the treatments with lower PS rate and mineral fertilizer before seeding (120 kg N ha−1) and complemented with topdressing mineral N. Thus, a sustainable strategy for inclusion of PS in rice fertilization is the application of moderate PS rates before seeding (≈120 kg N ha−1) complemented with mineral N topdressing.