© 2020 Biomolecular crystals are an emerging class of piezoelectric materials that are both biocompatible and biodegradable, which enables their use in biomedical applications and smart devices while ensuring eco-friendly production and disposal. However, accurate quantification of the piezoelectric response of soft sub-micron crystals remains a significant challenge, as conventional piezoelectric measurement techniques are suited to ceramics, thin films, and polymers. Here, we demonstrate the use of a novel piezoresponse force microscopy (PFM) methodology for robust, reliable quantification of the electromechanical response of biomolecular crystals. As a strong test of high accuracy and precision, we show that PFM, integrated with quantum mechanical (QM) density functional theory (DFT) calculations, can distinguish the piezoelectric responses of near-isopiezoelectric amino acid crystals. We show that a statistical approach, combined with experimental best practices, provides effective piezoelectric coefficients of biomolecular single crystals accurately and unambiguously. This work opens the door to high-throughput screening and characterisation of natural and engineered soft piezoelectric crystals for eco-friendly energy harvesters and biodegradable medical implants, reducing dependence on lead-based and rare-earth-containing piezoelectric materials.