The austral autumn transition represents a critical period linking the weakly nitrifying summer state to the enhanced winter nitrification regime in the Southern Ocean; however, observations during this period remain extremely limited. Here, we present the first investigation of seasonal variations in nitrate dual isotopes and nitrifying microbial abundances between summer and autumn in the Ross Sea to assess the recovery of nitrification during autumn. Relative to summer, mixed-layer nitrate isotopic signatures in autumn show little evidence for enhanced nitrification, indicating that nitrification in the autumn mixed layer remains weak. Meanwhile, ammonia-oxidizing bacteria abundances increase substantially from summer to autumn, whereas nitrite-oxidizing bacteria abundances, although elevated, remain comparatively low, suggesting asynchronous recovery within the nitrification pathway. Based on these in situ isotopic and microbial observations during the autumn transition, we propose that autumn nitrification in the Ross Sea represents a low-flux, incompletely recovered state in which the recovery of nitrite oxidation lags behind that of ammonia oxidation. These findings indicate that the recovery of upper-ocean nitrification lags behind seasonal environmental transitions in the Southern Ocean, providing new insight into seasonal transitions in Southern Ocean nitrogen cycling.