BACKGROUND: we assessed manager perceptions of food security and obesity in young children attending nurseries across England, assessing spatial differences by area-level deprivation. METHODS: we conducted an adjusted multinomial logistic regression and an adjusted geographically weighted logistic regression examining the odds of a manager perceiving obesity, food insecurity, or both as a problem among children in care measured via a mailed survey. RESULTS: 851 (54.3%) managers returned the survey. A nursery being in the highest tertile of area-level deprivation was associated with a 1.89 (95% CI 1.00, 3.57) greater odds of perceiving obesity as a problem, a 3.06 (95% CI 1.94, 4.84) greater odds of perceiving food insecurity as a problem, and a 8.39 (95% CI 4.36, 16.15) greater odds of perceiving both as a problem, compared with the lowest tertile. CONCLUSIONS: we observed differences in manager perception by area-level deprivation, but the relationship was especially pronounced for food insecurity.