Chickpea (Cicer arietinum L.) is the third most important food legume globally and is an important source of high-quality proteins to both humans and animals. It is highly sensitive to low temperature (LT) resulting in large scale yield losses. LT induces flower abortion in chickpea by disruption of gamete development and induction of pollen sterility. However, molecular mechanisms governing LT induced pollen sterility in chickpea are unknown. Disruption of carbohydrate metabolism has been implicated in LT induced damage to crops whereas proline and antioxidants protect plants from LT stress. In this study, the impact of LT on carbohydrates, proline and enzymatic antioxidants and expression of genes of these metabolite pathways were investigated in anthers at vacuolated pollen stage. The study included two genotypes, a cold-sensitive (GPF2) and a cold-tolerant (ICC 16349) that differed for pollen sterility under LT. Metabolite profiling revealed a reduction in starch and proline content in GPF2 under LT, whereas these parameters did not change but non-reducing sugars increased in ICC 16349. At the transcriptional level, cold initially lowered the transcription of all genes (19) under study in GPF2 and 14 genes out of 19 in ICC 16349. Initial down-regulation was followed by differential reactivation of transcription machinery in GPF2 and ICC 16349 at 30 min. Under LT, expression of starch synthesis, starch degradation, sucrose synthesis and sucrose transport genes showed a contrasting response in the two genotypes, where GPF2 showed downregulation of these genes while ICC 16,349 showed upregulation. The proline transport gene (proline transporter 1) showed higher downregulation in GPF2 than ICC 16349. Overall, pollen viability under LT in ICC 16349 was linked to the maintenance of starch, reducing sugars and proline levels and over-expression of UDP glucose pyrophosphorylase and cell wall invertase, while these processes were compromised in the GPF2 possibly leading to pollen sterility.