Morinda citrifolia L. is used as an alternative medicine in different parts of the world for treating various diseases including diabetes and heart diseases. As a functional food with a short shelf life, processing into different forms increases the shelf life while maintaining its biologically active metabolite and reducing pathogens; therefore, processing technology like natural fermentation must be well managed. The effect of prefermentation processing of noni juice extract on total flavonoid content (TFC), total phenolic content (TPC), total antioxidant activity (TAA), and antimicrobial activity for Escherichia coli and Staphylococcus aureus using minimum inhibitory concentration (MIC) was analyzed after subjecting noni fruits to 1%, 2%, and 3% of ascorbic acid and brine treatments and natural fermentation for 40 days, with the aluminum chloride calorimetric method at 420 nm for TFC, Folin–Ciocalteu reagent (FCR) at 650 nm for TPC, and 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) assay at 517 nm for TAA, where TFC ranged between 71.7 and 190.0 QE/mL, TPC between 62.6 and 63.7 mg GAE/mL, and TAA between 16.8% and 82.0%. Also, the pretreated noni extracts showed significant antimicrobial activity as compared to the untreated noni extract. In all, the pretreatments employed improved the bioactive compounds analyzed, but with variations.