Malaria and increasing parasite resistance necessitate new antiplasmodial agents and delivery systems. Senna siamea seeds contain bioactive metabolites, but their use is limited by poor solubility and instability. This study developed a chitosan-sodium alginate composite nanoemulsion containing S. siamea seed extract (JOHANEM-Bio), characterized its physicochemical properties and freeze-thaw stability, and evaluated its in vitro activity against Plasmodium falciparum 3D7. Seed powder was macerated with 96% ethanol, screened for phytochemicals, and formulated with virgin coconut oil, Tween 20, propylene glycol, chitosan, and sodium alginate using ultrasonication. Stability was assessed over six freeze-thaw cycles using one-way ANOVA. Antiplasmodial activity was evaluated at 0.01-100 µg/mL, and IC₅₀ was calculated by probit regression. Extraction yielded 12.8%, with alkaloids, tannins, polyphenols, and flavonoids detected. JOHANEM-Bio exhibited a particle size of 179.70nm±1.06, PDI of 0.27±0.00, zeta potential of -24.86mV±1.31, encapsulation efficiency of 67.27%±0.81, and spherical morphology. Freeze-thaw cycling increased particle size and PDI while reducing zeta-potential magnitude and encapsulation efficiency. Parasite inhibition reached 89.87%±0.53 at 100 µg/mL, with an IC₅₀ of 3.16 µg/mL versus 0.74 µg/mL for chloroquine. JOHANEM-Bio showed promising antiplasmodial activity, although further optimization, safety assessment, and in vivo validation are required.