The mechanisms through which livestock ownership is associated with childhood anaemia are contested. Using a cross-sectional, community-based survey of 300 households in southern Ghana, we determined the associations of household livestock ownership with anaemia among children aged 2–5 years. Potential mediating effects of animal-source food (ASF) consumption, microbial infections, and household food security were investigated. Data on each child's anaemia, malaria, and intestinal infections were collected for a subset of 221 households. Anaemia was defined as a haemoglobin (Hb) concentration <110 g/L. ASF consumption was measured as a count of the number of different ASF types consumed by each child in the week prior to the interview. Household food security was measured with a 15-item, pre-tested tool adapted from the USDA Household Food Security Core Module. The number of sheep and goats in aggregate was associated with higher odds of a child being anaemic (aOR (95% CI) = 1.10 (1.03, 1.17)). Households owning more free-range poultry had greater diversity of consumed ASFs among children (Coef. (95% C) = 0.02 (0.01, 0.03)). Owning more pigs was associated with higher odds that a household was food secure (1.05 (0.99, 1.12). We found no evidence that the child's ASF consumption mediated the association of livestock ownership with child anaemia, however,household food security mediated the association between household pig ownership and child anaemia. Overall, household ownership of livestock was associated with higher ASF consumption among children and improved household-level food security, yet also a higher odd of anaemia among those young children. The mechanisms leading to these seemingly counterintuitive relationships require further investigation.