Due to the heterogeneity among households across locations, predicting the impacts of stay-at-home mitigation and lockdown strategies for COVID-19 control is crucial. In this study, we quantitatively assessed the effects of the Namibia government's lockdown control measures on food insecurity in urban informal settlements with a focus on Windhoek, Namibia. We developed three types of conditional regression models to predict food insecurity prevalence (FIP) scenarios incorporating household frequency of food purchase (FFP) as the impacting factor, based on the Hungry Cities Food Matrix. Empirical data were derived from the 2017 African Food Security Urban Network (AFSUN) Windhoek study and applied univariate probit and bivariate partial observability models to postulate the relation between food insecurity and FFP within the context of stay-at-home disease mitigation strategy. The findings showed that FFP was positively correlated with the prevalence of food insecurity (r = 0.057, 95% CI: 0.0394, 0.085). Daily purchases portrayed a survivalist behaviour and were associated with increased food insecurity (coeff = 0.076, p = 0.05). Only those who were purchasing food twice monthly were significantly associated with reduced food insecurity (coeff = −0.201, p = 0.001). Those households in informal settlements were severely impacted by food insecurity (coeff = 0.909, p-value = 0.007). We conclude that public health compliance should precede with cash or food support to poor households in balance with the need for long-term placement of control measures to fully contain COVID-19 or related infectious diseases. [ABSTRACT FROM AUTHOR]