Biscuits contain high proportion of saturated fats, which could lead to an adverse health effect. The objective of this study was to study the functionality of complex nanoemulsion (CNE), which stabilised with hydroxypropyl methylcellulose and lecithin when used as a saturated fat replacer in short dough biscuits. Four biscuits formulations were studied including a control (butter), three formulations where 33% of the butter was replaced with extra virgin olive oil (EVOO), with CNE, and with the individual ingredient of the nanoemulsion added separately (INE). The texture properties, microstructure, and quantitative descriptive analysis with a trained sensory panel of the biscuits were evaluated. The results showed that CNE and INE gave place to doughs and biscuits with significantly higher (p < 0.05) hardness and fracture strength values than the control. The doughs made of CNE and INE showed significantly less oil migration during the storage than EVOO formulations, which confirmed by the confocal images. The trained panel did not find significant differences in crumb density and hardness on the first bite among CNE, INE and the control. In conclusion, nanoemulsion stabilised with HPMC and lecithin can work as a saturated fat replacer in short dough biscuits, providing satisfactory physical characteristics and sensory attributes.