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Seed maturation comprises important developmental processes, such as seed filling and the acquisition of seed germination capacity, desiccation tolerance, longevity, and dormancy. The molecular regulation of these processes is tightly controlled by the LAFL transcription factors, among which <i>ABSCISIC ACID INSENSITIVE 3 (ABI3)</i> was shown to be involved in most of these seed maturation processes. Here, we studied the <i>ABI3</i> gene from <i>Medicago truncatula,</i> a model legume plant for seed studies. With the transcriptomes of two loss-of-function <i>Medicago abi3</i> mutants, we were able to show that many gene classes were impacted by the <i>abi3</i> mutation at different stages of early, middle, and late seed maturation. We also discovered three <i>MtABI3</i> expression isoforms, which present contrasting expression patterns during seed development. Moreover, by ectopically expressing these isoforms in <i>Medicago</i> hairy roots generated from the <i>abi3</i> mutant line background, we showed that each isoform regulated specific gene clusters, suggesting divergent molecular functions. Furthermore, we complemented the <i>Arabidopsis abi3</i> mutant with each of the three <i>MtABI3</i> isoforms and concluded that all isoforms were capable of restoring seed viability and desiccation tolerance phenotypes even if not all isoforms complemented the seed color phenotype. Taken together, our results allow a better understanding of the ABI3 network in <i>Medicago</i> during seed development, as well as the discovery of commonly regulated genes from the three <i>MtABI3</i> isoforms, which can give us new insights into how desiccation tolerance and seed viability are regulated.