Protein–inorganic hybrid nanomaterials are a new type of functional materials that combine the advantages of inorganic and organic polymers and nanomaterials. We herein report a simple one-pot method for synthesizing organic–inorganic hybrid nanoflowers under mild biomineralization conditions using proteins as an organic component and lanthanide fluorides as an inorganic component. The as-prepared protein–rare earth fluoride nanoflowers exhibit high performance in maintaining enzyme stability and catalytic activity due to their high surface area and graded nanostructures, and have finely tunable luminescence properties of lanthanide ions. Various proteins such as trypsin, BSA, collagen and FtsZ have all displayed excellent capability to produce Na₅Yb₉F₃₂ nanoflowers, demonstrating that protein-templated biomineralization provides a universal and robust strategy for the synthesis of protein–rare earth fluoride hybrid nanoflowers. The novel luminescent protein–rare earth fluoride nanoflowers may have promising applications in biosensing, biocatalysis and medical diagnostics and treatment.