There is growing recognition of the need for fish to be better integrated into nutrition-sensitive strategies for addressing malnutrition. Fish are overwhelmingly produced by the small-scale sector, which supports food and nutrition security directly through the provision of fish and indirectly through the generation of income which can be used to purchase other desired foods. However, there has been relatively little research on the extent of food and nutrition security in specialised fishing communities. This study assessed food and nutrition security among households in specialised fishing communities in Komodo District, eastern Indonesia. We assessed the seasonal nutrition quality of household diets using the Food Consumption Score for nutritional analysis and food insecurity using the Household Food Insecurity Access Scale in 66 households across three communities, using a modified cluster sampling strategy. We calculated and generated descriptive statistics for these indicators with Microsoft Excel and ran a logistic generalized linear mixed model to determine factors associated with severe food insecurity using SPSS. We used semi-structured interviews and focus group discussions to understand perceptions of, change over time, and strategies for dealing with food shortfalls. While most households have acceptable access to nutritious foods, especially protein and heme iron-rich foods, nearly one half of households consumed vitamin A rich foods on less than 3 days of the 7-day recall period in either season. More than half of households reported experiencing a moderate or severe level of food insecurity, with higher food insecurity in the wet season. Low maternal education (OR: 3.8, 95%CI 1.5–9.9) and lower household wealth (OR: 0.5, 95%CI 0.3–0.9) were found to be associated with a severe level of food insecurity. Household’s consumptive and non-consumptive response strategies reflect adaptation to chronic food insecurity but are nutritionally and economically unsustainable. Households in specialised fishing communities in Komodo District consumed diets with low diversity and experienced high levels of food insecurity. There is a need for culturally-appropriate nutrition-sensitive strategies to enhance food and nutrition security in vulnerable fishing communities.