Armed insurgency and environmental degradation have pushed several people out of the rural communities of the Niger delta, and into the urban centers of the region. This massive migration caused the conversion of agricultural lands into other purposes, leading to fears of household food insecurity, especially among the indigenous population. This study compares the situation in a rural, and an urban community in Rivers State, one of the States in the Niger delta region of Nigeria. It used the Cornell-Radimer Food Security Scale to assess household food security and anthropometry to assess childhood malnutrition. A total of 204 questionnaires were administered and retrieved in both study communities, while the anthropometry of 332 under-five year children was taken. There were no significant differences in the age and household size of the respondents, but the respondents in the urban community were significantly better educated (p-value <0.001). The households in the urban community were also significantly better food secure (p-value < 0.005); and had significantly lower prevalence of wasting (p-value < 0.001), underweight (p-value < 0.005) and stunting (p-value < 0.001) than the households in the rural community. The indigenous population of the urban community was therefore better food secure, in spite of the loss of their farmlands to urbanization.