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This study uses nanoencapsulation with alginate-pectin beads to stabilize and control the release of coffee's cognitive-boosting aroma, which normally evaporates quickly. A nanoemulsion was created to improve encapsulation efficiency, with particle size measured by dynamic light scattering. FTIR and SEM were used to validate chemical interactions in the encapsulated beads. The release profiles showed that nanoemulsion-based alginate-pectin beads significantly reduced the initial burst release by approximately 60 % at the 14-h mark (from 88.09 % in control beads to 37.64 %). In silico studies were used to analyze volatile compounds discovered by gas chromatography–mass spectrometry (GC–MS/MS), including fatty acids, steroid derivatives, and 16-dehydropregnenolone acetate. The results showed interactions with Protein Kinase B (AKT1) and acetylcholinesterase (ACHE), indicating neuroprotection and cognitive improvement pathways. Increased cognitive control and arousal were shown in electroencephalography (EEG) investigations, with gamma wave relative power varying from baseline (9.74 ± 0.85 %) to during (11.03 ± 1.35 %) and post-inhalation (10.63 ± 1.06 %). Improved cognitive control and enthusiasm were seen. Advanced nanoencapsulation and molecular knowledge improve coffee aroma component stability, bioactivity, and controlled release in this study. This study reveals the molecular mechanisms and brain effects of encapsulated coffee aroma, providing a scientific basis for its potential neuroprotective properties and controlled-release applications.