Molecular clocks and daily feeding cycles support metabolism in peripheral tissues. Although the roles of local clocks and feeding are well defined at the transcriptional level, their impact on governing protein abundance in peripheral tissues is unclear. Here, we determine the relative contributions of local molecular clocks and daily feeding cycles on liver and muscle proteomes during the active phase in mice. LC–MS/MS was performed on liver and gastrocnemius muscle harvested 4 h into the dark phase from WT, Bmal1 KO, and dual liver- and muscle- Bmal1-rescued mice housed under 12 h light/12 h dark cycles with either ad libitum feeding or time-restricted feeding in the dark phase. Additional molecular and metabolic analyses were performed on liver and cultured hepatocytes. Feeding-fasting cycles had only minimal effects on liver and few, if any, on muscle. In contrast, Bmal1 KO altered the abundance of 674 proteins in liver and 80 proteins in muscle. Rescue of liver and muscle Bmal1 restored ∼50% of proteins in liver and ∼25% in muscle. These included proteins involved in fatty acid oxidation in liver and carbohydrate metabolism in muscle. For liver, proteins involved in de novo lipogenesis were largely dependent on Bmal1 function in other tissues (i.e., the wider clock system). Proteins regulated by BMAL1 in liver and muscle were enriched for secreted proteins. We found that the abundance of fibroblast growth factor 1, a liver secreted protein, requires BMAL1, and that autocrine fibroblast growth factor 1 signaling modulates mitochondrial respiration in hepatocytes. In liver and muscle, BMAL1 is a more potent regulator of dark phase proteomes than daily feeding cycles, highlighting the need to assess protein levels in addition to mRNA when investigating clock mechanisms. The proteome is more extensively regulated by BMAL1 in liver than in muscle, and many metabolic pathways in peripheral tissues are reliant on the function of the clock system as a whole. Display omitted •The clock gene Bmal1 regulates more proteins than time-restricted feeding at ZT16.•Liver de novo lipogenesis machinery requires clock function in other tissues.•Secreted proteins are enriched among Bmal1-regulated proteins.•Fibroblast growth factor 1 modulates mitochondrial respiration in hepatocytes via autocrine signaling. Circadian clock genes and feeding cycles regulate the transcriptome of metabolic tissues. Here, we used tandem mass tag labeling combined with LC–MS/MS to interrogate regulation of the proteome and show that, at nighttime, the effect of knocking out the molecular clock component Bmal1 is substantially greater than the effect of time-restricted feeding. In addition, we show that Bmal1-dependent proteins are enriched for secreted proteins, such as fibroblast growth factor 1, which modulates mitochondrial respiration in hepatocytes. Together, these results reveal layers of circadian regulation.