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Russet Burbank and Innovator are mid- to late-season frozen-processing cultivars with inherently different dormancy periods and susceptibilities to low temperature-induced sweetening (LTS). In contrast to Russet Burbank, which is highly prone to accumulation of reducing sugars (Glc + Fru) when stored below 8–9 °C, Innovator tubers exhibit moderate resistance to LTS and retain process quality longer at lower temperatures (4–6 °C). However, Innovator’s LTS resistance is not robust and often varies across production regions. Here we show that low O2 storage modulates LTS to reveal metabolic differences intrinsic to these cultivars. Changes in tuber respiration, process quality, reducing sugars, sucrose, starch phosphorylase and invertase activities were compared at 4 and 8 °C in 2.5 and 21 kPa O2 over a 212-d storage period. Tuber respiration declined rapidly as O2 level decreased from 21 to 2.5 kPa during acclimation at 8 °C. Respiration rates then fell further as the temperature was lowered from 8 to 4 °C, but this response was greatly muted for tubers at 2.5 versus 21 kPa O2. Tubers at 21 kPa O2 completed their cold-induced respiratory acclimation response (RAR) within 7 d compared with 13 d at 2.5 kPa O2, and the RAR was much greater for tubers at 2.5 kPa O2. While reducing sugars increased most rapidly in tubers over the first 30 d at 4 °C, Innovator tubers had lower invertase activity and sweetened less than Russet Burbank tubers, characterizing its LTS-resistant phenotype. Low O2 greatly attenuated these initial LTS responses for both cultivars; however, the effect was only temporary in Innovator. LTS resumed in Innovator tubers from 93 to 212 d with reducing sugar levels increasing to equal that of Russet Burbank tubers stored at 4 °C and 21 kPa O2. Activities of α-1,4 glucan phosphorylase (SP) were higher in Russet Burbank than Innovator and increased progressively over the storage period regardless of temperature and oxygen concentration. Innovator tubers stored at 2.5 kPa O2 had higher SP activities from 30 to 153 d at 4 and 8 °C compared with tubers stored at 21 kPa O2, which correlated well with increased sucrose buildup and earlier sprouting. The low O2-mediated inhibition of LTS was largely a consequence of reduced invertase activities.