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Molecular-based Fluorescent Organic Nanoparticles (FONs) are versatile light-emitting nano-tools whose properties can be rationally addressed by bottom-up molecular engineering. A challenging property to gain control over is the interaction of the FONs' surface with biological systems. Indeed, most types of nanoparticles tend to interact with biological membranes. To address this limitation, we recently reported on two-photon (2P) absorbing, red to near infrared (NIR) emitting quadrupolar extended dyes built from a benzothiadiazole core and diphenylamino endgroups that yield spontaneously stealth FONs. In this paper, we expand our understanding of the structure-property relationship between the dye structure and the FONs 2P absorption response, fluorescence and stealthiness by characterizing a dye-related series of FONs. We observe that increasing the strength of the donor end-groups or of the core acceptor in the quadrupolar (D-π-A-π-D) dye structure allows for the tuning of optical properties, notably red-shifting both the emission (from red to NIR) and 2P absorption spectra while inducing a decrease in their fluorescence quantum yield. Thanks to their strong 1P and 2P absorption, all FONs whose median size varies between 11 and 28 nm exhibit giant 1P (106 M−1.cm−1) and 2P (104 GM) brightness values. Interestingly, all FONs were found to be non-toxic, exhibit stealth behaviour, and show vanishing non-specific interactions with cell membranes. We postulate that the strong hydrophobic character and the rigidity of the FONs building blocks are crucial to controlling the stealth nano-bio interface. [ABSTRACT FROM AUTHOR]