Imaging is a critical step in diagnosis and therapy; thus, developing a non-carcinogenic near-infrared (NIR) emitting probe for guided therapy remains a priority for effective bacteria and cancer treatment. Herein, we report the effect of dual stabilization in producing NIR fluorescent CuInSe/ZnS quantum dots (QDs) and their use as imaging probes in cancer-bacteria therapy. The as-synthesised NIR QDs were stabilized using different combinations of hydrophilic dual capping agents, MPA-Gelatine, TGA-Gelatine, MPA-Citrate and TGA-Citrate. The optical characteristics of the prepared dual-stabilized CuInSe/ZnS QDs indicate that the material has high stability and fluorescence quantum yield. The dual stabilization resulted in varied emission positions as well as fluorescence intensity for the as-synthesized QDs. The cytotoxicity evaluation showed that cells treated with dual stabilised CuInSe/ZnS QDs displayed good cell viability against malignant fibrous histiocytoma-like (KM-Luc/GFP) cells, mouse colon carcinoma (C26) cells and mouse mammary carcinoma (FM3A-Luc) cells. It also showed high affinity to prostate and human adenocarcinoma cells with no indication of QDs uptake by normal prostate cells. The biofilm analysis showed that the QDs uptake was elevated in Staphylococcus aureus (Gram-positive bacteria) than in Escherichia coli (Gram-negative bacteria). The dual stabilized QDs remain a promising study as future fluorescence probes for early diagnosis and guided cancer therapy.