Mesenchymal stem cells (MSCs) have been researched for use in biomedical applications, particularly for cell-based therapies and regenerative medicine due to their self-renewing capacity and ability to differentiate into multiple cell types such as adipose, bone, and tendon tissues. Cryopreservation of MSCs is a common preservation method that is advantageous for cellular therapies in human and veterinary medicine. Adipose tissue-derived cells have been shown to maintain their properties after cryopreservation. In this study, we investigated the morphology, proliferation (cumulative population doubling level and doubling time), cell surface markers (CD34, CD90, and CD105), and ability to differentiate into adipose, bone, and cartilage tissues in vitro of equine adipose tissue-derived MSCs (eAD-MSCs) and miniature pig adipose tissue-derived MSCs (mpAD-MSCs) with and without long-term cryopreservation. The eAD-MSCs and mpAD-MSCs were analyzed immediately and after being frozen in liquid nitrogen for 3 years and 2 years, respectively. Cryopreserved eAD-MSCs maintained their morphology, proliferation rate, and cell surface markers compared with fresh cells. With the exception of proliferation rate, cryopreserved mpAD-MSCs also maintained their fresh cell characteristics. The proliferation rate of cryopreserved mpAD-MSCs was higher than that for fresh cells. Cryopreservation did not change the adipogenic, chondrogenic, or osteogenic differentiation potentials of eAD-MSCs and mpAD-MSCs. In summary, long-term cryopreservation maintains the cell phenotype and differentiation ability of eAD-MSCs and mpAD-MSCs. These results might be useful when developing veterinary medicine and clinical applications.