The morphological traits of alfalfa under acid soil conditions with different mobile aluminium (Al) concentrations were investigated. The study site was Vėžaičiai Branch of the Lithuanian Research Centre for Agriculture and Forestry, 55°70 N, 21°49 E. The experiment featuring the 30 most Al-tolerant alfalfa accessions (populations and cultivars), determined from laboratory trials was established on a Bathygleyic Dystric Retisol in 2018. In 2019 and 2020, the biological and morphological traits were evaluated: plant regrowth, plant height before flowering, wintering, leafiness, stem thickness, plant vigour, stem density, seed yield and resistance to spring black stem leaf spot. The resistance of alfalfa to mobile Al toxicity was determined using a filter-based screening method of selection cycles C1 and C2. The accessions grown in the soil with mobile Al (20.6–23.4 mg/kg) showed better tolerance to Al toxicity in the cycle C2. The hypocotyl tolerance index of these accessions was better at 8, 16, 32 and 64 mm AlCl3 concentrations in the cycle C2. The correlation analysis showed strong significant positive and negative relationships between the morphological traits. A cluster analysis showed that the accessions, grown in the soil with mobile Al (20.6–23.4 mg/kg) were the most resistant to Al toxicity in the cycle C2. These accessions produced a better seed yield and demonstrated lower values of morphological traits compared to cluster 2. Also, these accessions are considered as tolerant to mobile Al toxicity and might be used as donors in breeding for Al toxicity tolerance.