The medical community recommends that infant formulae should mimic human milk as far as possible, particularly in regards to long-chain polyunsaturated fatty acids (LC-PUFA). These include arachidonic acid (AA) and docosahexaenoic acid (DHA), both of which provide biochemical and functional benefits to neonates. However, LC-PUFAs are highly susceptible to oxidation and the composition of formulae must be carefully controlled. In this study, the stability of two types of LC-PUFA-supplemented milk-based powdered infant formula was evaluated over the course of 18 months storage at 25 °C and 40 °C. One contained egg yolk phospholipids (IF-EPL) and the other contained triacylglycerides (DHA and AA) synthesized by single cell oils (IF-SCO). The following parameters were monitored: peroxide values, volatile content (propanal, pentanal and hexanal), fatty acid profiles, and potential and free furfural content (5-hydroxymethyl-2-furaldehyde and 2-furaldehyde). In addition, these formulae were subjected to sensory evaluations by a panel of experts. The parameters studied revealed acceptable lipid stability in both types of formula, with better results for IF-EPL. At the end of the study period, significant deficits (p < 0.05) in linoleic acid were noted in both formulae. However, no significant decreases were observed in the other fatty acids, including AA and DHA. In regards to furfural content, both formulae exhibited a similar increase, indicative of the typical Maillard reaction characteristic of products stored for long periods.