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Concerns have been raised about the usage of sodium hypochlorite (NaOCl) in endodontics following its toxic effects. Effective ecoproduce (EEP), an organic solution produced through the fermentation of fruit peels, exhibits antibacterial and antibiofilm action, suggesting its potential as an endodontic irrigant. However, studies on its cytotoxicity are limited. This in vitro study aimed to evaluate the cytotoxic effects of EEP at different concentrations and fermentation periods against the MC3T3-E1 cell. EEP derived from orange and pineapple peel waste and fermented for 3 and 6 months was prepared from 100% to 0.78% concentration. Briefly, 2.5% NaOCl was used as the comparison group. Cell viability was analysed using Alamar Blue and Live and Dead Cell assay. A transmission electron microscope (TEM) was used to evaluate ultrastructural changes to the cells. Data analysis was performed using a two-way mixed Analysis of Variance (ANOVA). EEP exhibited concentration-dependent cytotoxicity regardless of the fermentation period (p > 0.05). A concentration below 6.25% was non-cytotoxic and comparable to the negative control (p > 0.05). Live and Dead Cell assay and TEM analysis complement the findings. The mean cell viability of EEP at all concentrations for both fermentation periods was significantly higher than that of 2.5% NaOCl (p < 0.05). Conclusively, 6.25% EEP fermented for 3 and 6 months are non-cytotoxic and can serve as an alternative endodontic irrigants. Full article