In this work, the utilization of phosphogypsum (PG), a waste coming from the manufacture of phosphate fertilizers, as fertilizer for alfalfa (Medicago sativa L.) crops was investigated using pot experiments. The objective of this study was to evaluate the effects of both phosphogypsum and red mud (RM) in two soils representative of the pasture production area in Southern Spain. The morpho-physiological parameters of biomass, plant height, number of stems and number of leaves, as well as the chemical parameters of soil content, were measured. High doses of PG inhibited seed germination in some treatments. In addition, the treatment substrate (2550 g soil + 50 g kg−1 PG + 100 g kg−1 RM) also affected seed germination, possibly due to the large amount of RM. The application of PG and RM to the soil increased the availability of important nutrients for alfalfa, such as phosphorus (P), calcium (Ca2+) and magnesium (Mg2+). The results demonstrate that the treatment with PG significantly improved the uptake of P in alfalfa.