Molybdenum (Mo) in basic soils has high bioavailability and plant toxicity. This study aimed to investigate the effect of increasing Mo concentration on its availability and toxicity threshold in alfalfa plants grown in sandy loam calcareous soils, and the potential use of raw and acid- modified clay deposits as soil additives to immobilize Mo and reduce its phytoavailability. Raw clay deposits (RCD) were treated with H2SO4 to produce acid-modified clay deposits (AMCD). The first experiment was performed using soils treated with 0, 0.1, 1, 10, 50, and 100 mg Mo kg−1. The second experiment was conducted with soils treated with 10 or 50 mg Mo kg−1 and amended with RCD and AMCD at application rates of 0, 2.5, 5, and 10% (w/w). After harvesting, water-soluble Mo, ammonium bicarbonate-diethylenetriaminepentaacetic acid (AB-DTPA)-extractable Mo, and shoot Mo content as well as dry matter were measured. The results showed that water-soluble Mo, AB-DTPA-extractable Mo, and shoot Mo concentration increased at higher Mo soil addition. AMCD had a stronger influence on Mo immobilization and reduction effect on plant shoots compared to RCD, depending on soil Mo concentration and application rate. Applying AMCD decreased soil pH but increased salinity levels. The shoot dry matter significantly increased in soils amended with RCD and/or AMCD compared to control soils; with the highest improvement recorded for RCD at 10%. It was concluded that AMCD is an efficient immobilizing agent to reduce Mo mobility and its phytoavailability in calcareous soils. Additionally, both AMCD and especially RCD were able to create favorable conditions for plant growth.