High hydrostatic pressure (HHP) is a non-thermal process widely used in the food industry to reduce microbial populations. However, rarely its effect has been assessed in products with high oil content. This study evaluated the efficacy of HHP (200, 250, and 300 MPa) at different temperatures (25, 35, and 45 °C) by cycles (1, 2, or 3) of 10 min in the inactivation of Aspergillus niger spores in a lipid emulsion. After treatments at 300 MPa for 1 cycle at 35 or 45 °C, no surviving spores were recovered. All treatments were modeled by the linear and Weibull models. The presence of shoulders and tails in the treatments at 300 MPa at 35 or 45 °C resulted in sigmoidal curves which cannot be described by the linear model, hence the Weibull + Tail, Shoulder + Log-lin + Tail, and double Weibull models were evaluated to elucidate the inactivation kinetics. The tailing formation could be related to the presence of resistance subpopulations. The double Weibull model showed better goodness of fit (RMSE <0.2) to describe the inactivation kinetics of the treatments with the higher spore reductions. HHP at 200–300 MPa and 25 °C did not reduce the Aspergillus niger spores. The combined HHP and mild temperatures (35–45 °C) favored fungal spore inactivation. Spore inactivation in lipid emulsions by HHP did not follow a linear inactivation. HHP at mild temperatures is an alternative to the thermal process in lipid emulsions.