AbstractInorganic nanohosts doped with lanthanide ions are an indispensable tool for multimodal bioimaging and MRI applications due to their distinctive optical, magnetic, and biocompatible properties. Nanocomposites of such nanoprobes with functionalization capabilities could also enable their use in targeted therapy‐based applications. However, the influence of nanocomponents especially their proportion in a nanocomposite in modulating the physio‐chemical and biocompatibility properties of the nanocomposite is still elusive. To address this knowledge gap, we have engineered nanocomposites variants using an environmentally benign one‐step synthesis with ionic liquids. We have synthesized two nanocomposites, differing in the proportion of lanthanide‐doped ternary fluoride nanoparticles (as nanophase material with luminescent and magnetic traits) and graphene oxide (as host matrix phase with tunable functionalization potential for theranostics applications). We found that with increased GO nanomaterial, nanocomposites showed reduced crystallite size and photoluminescence properties without significantly affecting the magnetic traits. Thus, implying nanocomponents ratio has differential effect on the nanocomposite properties. To assess biocompatibility, we have employed sensitive biomarkers such as craniofacial development, cardiac rhythm, and overall survivability of zebrafish larvae. Remarkably, biocompatibility improved when the proportion of the GO was increased within the nanocomposite as compared to when the nanocomponents were assessed individually. Our results also revealed that biocompatibility of nanocomposites also depends on the synergistic interplay between the nanocomponents due to the spatial arrangement of each nanocomponent in the nanocomposites. Overall, our study offers an intriguing avenue for tuning the biocompatibility of such nanocomposites, rendering them as an application‐independent biocompatible‐platform for theranostics applications.