The successful development of highly sensitive, water-compatible, nontoxic nanoprobes has allowed nanomaterials to be widely employed in various applications. The applicability of highly bright quantum dot (QD)-based probes consisting of QDs on 120 nm silica nanoparticles (NPs) with silica shells is investigated. Their substantial merits, such as their brightness and biocompatibility, for effective bioimaging are demonstrated. Silica-coated, QD-embedded silica NPs (Si@QDs@Si NPs) containing QDs composed of CdSe@ZnS (core-shell) are prepared to compare their structure-based advantages over single QDs that have a similar quantum yield (QY). These Si@QDs@Si NPs exhibit approximately 200-times stronger photoluminescence (PL) than single QDs. Cytotoxicity studies reveal that the Si@QDs@Si NPs are less toxic than equivalent numbers of silica-free single quantum dots. The excellence of the Si@QDs@Si NPs with regard to in vivo applications is illustrated by significantly enhanced fluorescence signals from Si@QDs@Si-NP-tagged cells implanted in mice. Notably, a more advanced version of QD-based silica NPs (Si@mQDs@Si NPs), containing multishell quantum dots (mQDs) composed of CdSe@CdS@ZnS, are prepared without significant loss of QY during surface modification. In addition, the Si@mQDs@Si NPs display a fivefold higher fluorescence activity than the Si@QDs@Si NPs. As few as 400 units of Si@mQDs@Si- NP-internalized cells can be detected in the cell-implanted mouse model.