(1) Background: Working night shifts has been associated with altered circadian rhythms, lifestyle habits, and cardiometabolic risks. No information on the potential association of working shift and the presence of atherosclerosis is available. The aim of this study was to quantify the association between different work shifts and the presence of subclinical atherosclerosis objectively measured by imaging. (2) Methods: Analyses were conducted on the baseline data of the Aragon Workers Health Study (AWHS) cohort, including information on 2459 middle-aged men. Categories of shift work included central day shift, rotating morning-evening or morning-evening-night shift, and night shift. The presence of atherosclerotic plaques was assessed by 2D ultrasound in the carotid and femoral vascular territories. Multivariable logistic models and mediation analysis were conducted to characterize and quantify the association between study variables. (3) Results: Participants working night or rotating shifts presented an overall worse cardiometabolic risk profile, as well as more detrimental lifestyle habits. Workers in the most intense (morning-evening-night) rotating shift presented higher odds of subclinical atherosclerosis (odds ratio: 1.6; 95% confidence interval: 1.12 to 2.27) compared to workers in the central shift, independently of the presence of lifestyle and metabolic risk factors. A considerable (21%) proportion of this association was found to be mediated by smoking, indicating that altered sleep-wake cycles have a direct relationship with the early presence of atherosclerotic lesions. (4) Conclusions: Work shifts should be factored in during workers health examinations, and when developing effective workplace wellness programs.