Diamond nanoparticles that host bright luminescent centers are attracting attention for applications in bio-labeling and bio-sensing. Beyond their unsurpassed photostability, diamond can host multiple color centers, from the blue to the near infra-red spectral range. While nanodiamonds hosting nitrogen vacancy defects have been widely employed as bio-imaging probes, production and fabrication of nanodiamonds with other color centers is a challenge. In this work, a large scale production of fluorescent nanodiamonds (FNDs) containing a near infrared (NIR) color center - namely the silicon vacancy (SiV) defect, is reported. More importantly, a concept of application of different color centers for multi-color bio-imaging to investigate intercellular processes is demonstrated. Furthermore, two types of FNDs within cells can be easily resolved by their specific spectral properties, where data shows that SiV FNDs initially dispersed throughout the cell interior while NV FNDs localized in a close proximity to nucleus. The reported results are the first demonstration of multi-color labeling with FNDs that can pave the way for the wide-ranging use of FNDs in applications, including bio-sensing, bio-imaging and drug delivery applications.