The quality of acclimatized in vitro cultivated plants is essential to ensure good survival and growth after planting in field conditions. After two months of acclimatization, this study revealed a significant variation in survival rate, shoot characteristics, root traits, and biomass features between 13 clones of Melia volkensii Gürke. A number of quality indices such as the Dickson Quality Index (DQI), shoot dry weight: root dry weight ratio (S:R), and sturdiness quotient (SQ) also showed a large variation. The survival rate was genotype-dependent, with an average of 85%. Extreme genotypes were tall, had long internodes, a lot of leaves, and a large leaf area. At the other side of the spectrum, there were small clones with short internodes and a reduced number of leaves and leaf areas. The high S:R values (>2) of the evaluated clones indicate an imbalance between the shoot and root system, negatively influencing the quality of the in vitro produced M. volkensii plants. The SQ for all clones was below the threshold value of 6, implying a good and expected survival rate. This study illustrates that some clones might systematically score better for SQ, S:R, plant volume, and DQI after acclimatization and that these factors could form the basis for selection.