Among the adenylate carriers identified inArabidopsis thaliana, only the AMP/ATP transporterADNT1shows increased expression in roots under waterlogging stress conditions. Here, we investigated the impact of a reduced expression ofADNT1inA. thalianaplants submitted to waterlogging conditions. For this purpose, anadnt1T-DNA mutant and twoADNT1antisense lines were evaluated. Following waterlogging,ADNT1deficiency resulted in a reduced maximum quantum yield of PSII electron transport (significantly foradnt1and antisense Line 10), indicating a higher impact caused by the stress in the mutants. In addition,ADNT1deficient lines showed higher levels of AMP in roots under nonstress condition. This result indicates that the downregulation ofADNT1impacts the levels of adenylates.ADNT1-deficient plants exhibited a differential expression pattern of hypoxia-related genes with an increase in non-fermenting-related-kinase 1 (SnRK1) expression and upregulation of adenylate kinase (ADK) under stress and non-stress conditions. Together, these results indicated that the lower expression ofADNT1is associated with an early “hypoxic status” due to the perturbation of the adenylate pool caused by reduced AMP import by mitochondria. This perturbation, which is sensed by SnRK1, results in a metabolic reprogramming associated with early induction of the fermentative pathway inADNT1deficient plants.