Nucleus pulposus (NP) cells reside in an avascular and hypoxic microenvironment of the intervertebral disc and are predominantly glycolytic due to robust HIF‐1 activity. It is generally thought that NP cells contain few functional mitochondria compared with cells that rely on oxidative metabolism. Consequently, the contribution of mitochondria to NP cell metabolism and the role of hypoxia and HIF‐1 in mitochondrial homeostasis is poorly understood. Using mitoQC reporter mice, we show for the first time to our knowledge that NP cell mitochondria undergo age‐dependent mitophagy in vivo. Mechanistically, in vitro studies suggest that, under hypoxic conditions, mitochondria in primary NP cells undergo HIF‐1α‐dependent fragmentation, controlled by modulating the levels of key proteins DRP1 and OPA1 that are involved in mitochondrial fission and fusion, respectively. Seahorse assays and steady state metabolic profiling coupled with [1‐2‐13C]‐glucose flux analysis revealed that in hypoxia, HIF‐1α regulated metabolic flux through coordinating glycolysis and the mitochondrial TCA cycle interactions, thereby controlling the overall biosynthetic capacity of NP cells. We further show that hypoxia and HIF‐1α trigger mitophagy in NP cells through the mitochondrial translocation of BNIP3, an inducer of receptor‐mediated mitophagy. Surprisingly, however, loss of HIF‐1α in vitro and analysis of NP‐specific HIF‐1α null mice do not show a decrease in mitophagic flux in NP cells but a compensatory increase in NIX and PINK1‐Parkin pathways with higher mitochondrial number. Taken together, our studies provide novel mechanistic insights into the complex interplay between hypoxia and HIF‐1α signaling on the mitochondrial metabolism and quality control in NP cells.