Breast tumor heterogeneity is responsible for the death of ~ 40,000 women in 2017 in USA. Triple-negative breast cancers (TNBCs) are very aggressive and it is the only breast cancer subgroup still lacking effective therapeutic. As a result, early stage detection of TNBC is vital and it will have huge significant in the clinics. Driven by the need, here we report the design of highly crystalline antibody-conjugated multifunctional multicolor luminescence nanosystem derived from naturally available popular tropical fruits mango and prune, which have capability to track breast cancer heterogeneity via selective separation and accurate identification of TNBC and HER-2 (+) or ER/PR (+) breast cancer cells selectively and simultaneously. A detailed synthesis and characterization of multifunctional multicolor nanosystems from tropical fruits has been reported. Experimental results show that by changing the fruits, multicolor luminescent carbon dots (LCDs) can be developed and is mainly due to the formation of highly crystalline nano dots with different heavy metal doping and also due to the presence of different types of surface functional groups. Experimental data presented show that multifunctional multicolor nanoprobe can be used for highly selective and simultaneous capturing of targeted TNBCs, HER2(+) or ER(+) breast cancer cells and the capture efficiency can be as high as 98%. Reported data indicate that multicolor fluorescence imaging can be used for mapping hetergenous breast cancer cells simultaneously, and it can distinguish targeted TNBCs from non-targeted HER-2 (+) or ER/PR (+) breast cancer. Our finding suggests excellent possibility of designing multicolor nanosystems from natural fruits for tracking cancer heterogeneity in clinics.