Pharmaceutical companies worldwide are scrambling to develop new ways to combat cancer and microbiological pathogens. The goal of this research was to investigate the antibacterial, anticancer, and apoptosis effects of novel niosomal formulated Persian Gulf Sea cucumber extracts (SCEs). Sea cucumber methanolic extracts were prepared and encapsulated in niosome nanoparticles using thin-film hydration. The compound was made up of Span 60 and Tween 60 blended with cholesterol in a 3:3:4 M ratios. Characterization of niosome-encapsulated SCE evaluated by scanning electron microscopy and transmission electron microscopy. The disk diffusion method and microtiter plates were used to investigate the antimicrobial activity. The effect of niosome-encapsulated SCE on cell proliferation and apoptosis induction was studied using MTT and Annexin V, respectively. The expression of apoptosis-related genes, including Bax, Fas, Bax, Bak, and Bcl2, was studied using quantitative real-time PCR. Niosome-encapsulated SCE with a size of 80.46 ± 1.31 and an encapsulation efficiency of 79.18 ± 0.23 was formulated. At a concentration of 100 μg/ml, the greatest antimicrobial effect of the niosome-encapsulated SCE was correlated to Staphylococcus aureus, with an inhibition zone of 13.16 mm. The findings of the study revealed that all strains were unable to produce biofilms at a concentration of 100 μg/ml niosome-encapsulated SCE (p < 0.001). The survival rate of cancer cells after 72 h of exposure to niosome-encapsulated SCE was 40 ± 3.0%. Encapsulated SCE in niosomes inhibited cell progression in MCF-7 cells by increasing G0/G1 and decreasing S phase relative to G2/M phase; as a result, it activated the apoptosis signaling pathway and led to the induction of apoptosis in 69.12 ± 1.2% of tumor cells by increasing the expression of proapoptotic genes (p < 0.001). The results indicate that sea cucumber species from the Persian Gulf are a promising source of natural chemicals with antibacterial and anticancer properties, paving the path for novel marine natural products to be discovered. This is the first demonstration that niosome-encapsulated SCE contains antibacterial and anticancer chemicals that, according to their specific characteristics, boost antitumor activity.