A cheap method allowing fabrication of biocompatible, ultra-small (2–10 nm) and fluorescent (λem = 425–500 nm) nanohybrids (NHs) from coffee wastes is reported. The gadolinium-doped nanohybrids (GDNHs) or gadolinium-free carbon dots (GFCDs) can be synthesized in a domestic microwave oven according to green synthesis principles. Hydrodynamic sizes, chemical composition, impact on proton magnetic resonance relaxation time and optical properties of the GDNHs and GFCDs were studied in details and compared. In particular, doping of the NHs with Gd3+ ions, up to 1.87 % w/w of gadolinium per particles’ weight, will allow their application for magnetic resonance imaging (MRI). Furthermore, cell culture tests on human adenocarcinomic alveolar basal epithelial cells line (A549) have shown high biocompatibility of the GDNHs and in a wide concentration range 100–1000 µg/ml.