The circadian clock plays a key role in regulating the timing of plant development. Despite its immense potential contribution to yield-related traits, the wheat (Triticum aestivum) clock has received little focus. Here, we measured circadian rhythms of elite Australian wheat cultivars and identified a large variation in the clock’s output between genotypes. We show that the cycling pace (period) of these cultivars covaries with the timing of leaf senescence and leaf-to-grain nutrient mobilisation. To investigate how the clock might govern these traits, we generated 48-hour ‘circadian transcriptomes’ in mature and senescent wheat flag leaves. The period of rhythmic transcripts shortens by an average of 0.5 h in senescent leaves, akin to observations of ageing in other organisms. Strikingly, clock genes are enriched amongst a set of transcripts that show little or no change in period with senescence (within ±0.5 h). We clustered clock genes by specific changes in their transcript rhythms in senescent flag leaves, revealing a multifaceted transcriptional response of the clock at senescence. Genetic variation associated with each transcriptional response was used to group a 283-cultivar wheat diversity panel into six haplotypes. Circadian period, senescence and grain yield differed significantly between haplotypes. Moreover, a deletion in the clock gene EARLY FLOWERING 3 (TaELF3-1D) within pairs of near-isogenic lines (NILs) was shown to accelerate senescence and reduce grain protein content. Our findings highlight the untapped functional potential of clock gene variation in wheat and outline a genetic basis for a connection between the clock, senescence, and grain nutrition.