Malaysian children often skip breakfast, an important meal providing essential nutrients for optimal growth and maintaining proper nutritional status. Therefore, this study aims to investigate the associations between breakfast skipping with dietary intake, diet quality, and adiposity indicators among primary schoolchildren aged 6.0–12.9 years. This study involved 1383 children from the South East Asian Nutrition Surveys (SEANUTS II) Malaysia. Information collected through questionnaires included sociodemography and breakfast consumption, defined as the first meal before noon. Breakfast skipping was identified as skipping breakfast at least once a week. Anthropometric measures, including height, body weight, and waist circumference, as well as percentage of body fat, were collected. Body mass index (BMI) and waist-to-height ratio were calculated, and BMI-for-age-z-scores was determined using WHO (2007) growth reference. A one-day 24-hour dietary recall was employed to assess dietary intake, and diet quality was analyzed using Malaysian Healthy Eating Index. Binary logistic regression was applied to examine relationship between breakfast skipping on diet quality and adiposity indicators. Over one-third (36.0%) of children skipped breakfast at least once a week, resulting in lower intakes of energy, nutrients, cereals/grains, vegetables, and milk/dairy products, though not affecting total diet quality score. Breakfast skipping was associated with higher odds of overweight/obesity (aOR 2.04, 95%CI: 1.52–2.76) and central obesity (aOR 1.87, 95%CI 1.34–2.61). In conclusion, primary schoolchildren in Peninsular Malaysia who skipped breakfast tended to have lower consumption of nutrients and specific basic food groups, as well as increased body fat. This study highlights the importance of continuing to educate parents and children about healthy eating habits, especially the need to adhere to dietary recommendations, with an emphasis on breakfast consumption.