Meals are an important source of food intake, contributing to body weight and health status. Previous studies have examined the relationship between isolated mealtime behaviours and the metabolic syndrome (MetS). The aim of this study was to examine the influence over time of ten interrelated mealtime habits on the risk of developing the MetS and insulin resistance (IR) among Mexican adults. We conducted a prospective cohort study with a sample of 956 health workers. The Mealtime Habits Quality (MHQ) scale is based on four mealtime situations (availability of time to eat, distractions while eating, environmental and social context of eating, and familiar or cultural eating habits), which were used to assess the participants’ MHQ at the baseline (2004–2006) and follow-up (2010–2012) evaluations. The MetS was assessed using criteria from the National Cholesterol Education Program Adult Treatment Panel III (NCEP-ATP III) and the International Diabetes Federation (IDF). IR was defined using the homoeostasis model assessment. Crude and adjusted relative risks were calculated to estimate the relationship between MHQ and the risk of developing the MetS or IR. Participants classified in the lower MHQ category had an 8·8 (95 % CI 3·1, 25) and 11·1 (95 % CI 3·4, 36·1) times greater risk of developing the MetS (using the NCEP-ATP III and IDF criteria, respectively), and an 11·2 times (95 % CI 3·9, 31·5) greater likelihood of developing IR, compared with those in the higher MHQ group. This prospective study reveals that individuals who engaged in more undesirable than recommended mealtime behaviours had a >10-fold risk of developing the MetS or IR.