Food security (FS) is a function of food availability, accessibility, stability and utilization. Food value chains (FVCs) are part of the food system and are characterized by five main components: natural resources, food production, processing, markets and consumption. Many methods are available to assess single FVC components, but few cover a series of FVC components. This paper introduces an integrated research framework which combines both qualitative and quantitative methodologies across a generic FVC. Furthermore, this approach provides mechanisms to identify the contribution to FS of each component in the FVC. The methodology uses an FVC as an analytical framework within which to assess FS in a systematic approach. Starting with a working scenario, each tool was evaluated according to its potential to assess FS indicators in different components, and then classified according to its temporal and spatial scales. The advantages, challenges and limitations of this conceptual approach are evaluated and discussed.