Inadequate diet influences chronic diseases such as cardiovascular disease (CVD), the leading cause of death in Spain. CVD figures vary from one geographical region to another; this could be associated with different food choices. Our aim was to analyse the influence of geographical area on nutrient intakes among the Spanish adult population with Metabolic Syndrome (MetS). We analysed cross-sectional baseline data from the PREDIMED-Plus study: 6646 Spanish adults, aged 55–75 years, with overweight/obesity and MetS in four geographical areas. A validated 143-item Food Frequency Questionnaire (FFQ) was used to assess energy and nutrient intakes. The prevalence of inadequate nutrient intake was estimated according to Dietary Reference Intakes (DRIs). Multivariable-adjusted logistic regression was used to assess the relationship between geographical area (North, Central, East and South areas) and inadequate nutrient intake. People in the North area consumed significantly lower amounts of vegetables and fish but more sugar and alcohol (p < 0.001) than other areas. Dietary fibre, vitamin A, E, calcium and magnesium intakes were all lower among men of North area than in the other areas (p < 0.001). Sex (women), non-smoker and physical activity were also associated to adequate nutrient intake. Geographical area influences nutrient intakes. Its effect on dietary quality should be taken into account when planning food policies.