A dietary pattern transition is a risk factor for the double burden of malnutrition (DBM), but related information is limited. This study aimed to identify sex differences in dietary patterns of adults in a low-middle income country and to examine their association with DBM. A total of 8957 adults (4465 men and 4492 non-pregnant and non-lactating women) who participated in the 2013 Philippine National Nutrition Survey were included in the analysis. Logistic regression models were formulated to investigate the relationship between dietary patterns and DBM. The factor analysis derived seven dietary patterns for males and six patterns for females. Results showed that approximately 30% of Filipino adults suffered from DBM. The rice pattern was associated with lower odds of DBM for males only. The meat and sugar pattern in males and the protein-rich foods, cereal, and sugar pattern in females decreased DBM likelihood. An inverse relationship was observed for the vegetables and corn patterns, wherein females had an increased risk for DBM. Our findings suggest that rice-based and meat-containing patterns could play protective roles in DBM development among adults in the Philippines. Understanding sex-specific dietary patterns can be utilized to guide public health nutrition interventions in the prevention of malnutrition in all its forms.