The Rubber Hand Illusion (RHI) creates distortions of body ownership through multimodal integration of somatosensory and visual inputs. This illusion largely rests on bottom-up (automatic multisensory and perceptual integration) mechanisms. However, the relative contribution from top-down factors, such as controlled processes involving attentional regulation, remains unclear. Following previous work that highlights the putative influence of higher-order cognition in the RHI, we aimed to further examine how modulations of working memory load and task instructions—two conditions engaging top-down cognitive processes—influence the experience of the RHI, as indexed by a number of psychometric dimensions. Relying on exploratory factor analysis for assessing this phenomenology within the RHI, our results confirm the influence of higher-order, top-down mental processes. Whereas task instruction strongly modulated embodiment of the rubber hand, cognitive load altered the affective dimension of the RHI. Our findings corroborate that top-down processes shape the phenomenology of the RHI and herald new ways to improve experimental control over the RHI.