Amino acid‐based biomolecular glasses represent an emerging material to meet the demand for sustainable development. However, most amino acids are difficult to vitrify due to their strong crystallization tendency, limiting further advancements of this field. In this study, we demonstrate that the introduction of counterions effectively suppresses crystallization, as hydrogen bonds within the system stabilize the disordered structures. Based on this, we propose a counterion co‐assembly strategy to synthesize a wide range of amino acid‐based glasses. This strategy enables the facile fabrication of glass with customizable shapes, high mechanical rigidity, and tunable multicolor fluorescence, ranging from blue to red depending on the excitation wavelength. Furthermore, this strategy allows the integration and enhancement of counterion properties within the glass matrix. Through the co‐assembly of phosphorescent counterions, we synthesized a series of long‐persistent luminescent glasses with significantly extended afterglow lifetimes. This work presents an effective approach for the synthesis of amino acid‐based glasses and provides insights into the development of supramolecular glasses with tailored functionalities.