To effectively assess and maintain animal well-being, reliable and accessible indicators are crucial. Researchers have proposed using rhythmicity as a measure of animal welfare. An animal in a good state of welfare would, ideally, follow the same daily rhythmic patterns while disruptions in these patterns may signal stress or illness. Although promising in certain cases, it remains unclear how rhythmicity reflects the well-being of animals in managed husbandry systems, where external (human) factors might impact their rhythmicity. This study investigated how extrinsic factors, such as feeding times, affect the rhythmicity of domesticated horses, aiming to assess its value as a welfare indicator. Twenty horses, of which 18 were included in the final analysis, were allocated to four groups and exposed to three feeding regimes according to a randomized crossover design: three 2-hour feeding periods during daylight hours, six 1-hour feeding periods distributed over 24 hours, and ad libitum access to hay through a slow-feeding net. Continuous acceleration-derived activity data were recorded using accelerometers attached to the horses’ left front legs. The resulting time-series data were used to determine lying duration based on the orientation of the accelerometer’s y-axis. The data were also analysed using Fourier transformation to calculate the Degree of Functional Coupling (DFC), which quantifies the temporal organisation of the horses’ daily locomotor activity patterns and the extent to which these patterns are coupled to periodic environmental cues; it does not represent the animals’ overall biological rhythmicity. We established a linear mixed-effects model with DFC as the response variable. Bayesian Information Criterion-based model selection revealed that lying duration and feeding regime were the most effective predictors of DFC. Our analysis showed a significant effect of the experimentally imposed feeding schedules on the temporal organisation of the horses’ daily locomotor activity patterns. In conclusion, activity-derived DFC should be interpreted cautiously in managed husbandry systems. Extrinsic factors that impose or reinforce rhythmic locomotor activity patterns should be considered when comparing DFC across systems.