Circadian rhythms are ubiquitous to life and are the most pervasive rhythm in nature; from bacteria to plants and animals, most organisms demonstrate daily physiological, behavioural, and metabolic cycles. Akin to other vertebrates, fish gut microbiota is critical to nutritional provision, metabolic homeostasis, and immune defence and it is evident that metabolism, circadian rhythms of activity and the gut microbiome are inextricably intertwined. As the aquaculture industry turns towards augmentation of fish microbiomes to promote health and productivity, it is suggested that a chronobiological understanding of fish microbiomes and feed treatment times may be crucial for their effectiveness and is necessary to ensure sustainable aquaculture nutrition and fish health. Using experimental feed trials, daily activity assays, and 16S rRNA microbiome profiling, I examined the effect of feed timing on rainbow trout growth, behaviour, and gut microbiome composition and daily rhythms. This study indicates that feed timing has no strong impact on growth, although trout fed early in the light cycle appeared to have a dampened circadian clock. Early fed fish displayed arrhythmic daily activity patterns and fewer gut microbial taxa exhibited rhythmicity in abundance. This dampening of the endogenous circadian clock of the host organism may be detrimental for fish welfare by perturbing the commensal microbiome, potentially instigating resounding effects on the functional pathways of microbiota and consequently fish health.