Food security is one of the major concerns in the Philippines. Although livestock and poultry production accounts for a significant proportion of the country’s agricultural output, smallholder households are still vulnerable to food insecurity. The current study aims to examine how livestock production and selling difficulties affect smallholder households’ food-insecure conditions. For this objective, Bayesian Mindsponge Framework (BMF) analytics was employed on a dataset of the Food and Agriculture Organization’s Data in Emergencies Monitoring (DIEM) system. We found that production and selling difficulties significantly adversely affect food insecurity in the Philippines. However, their effects vary according to the severity of food insecurity. In particular, production and selling difficulties affect the households’ likelihood of eating less healthy and nutritious food equally. However, the production difficulties have more negligible impacts on the possibility of skipping meals and even ambiguous impacts on the likelihood of not eating for a whole day compared to the effects of selling difficulties. Moreover, we also found that the market plays a crucial role in facilitating not only livestock trading but also livestock production (e.g., purchase of feed and medicines). Based on these findings, we suggest that the livestock market needs to be expanded and regulated to maintain the balancing prices between livestock products and products and services used for livestock production, and facilitate the product-exchanging mechanism.