Phosphonate natural products, characterized by a stable carbon–phosphorus (C–P) bond, represent a distinctive class of natural products with broad bioactivities and diverse applications in medicine and agriculture. Despite their potential, the field has lacked a systematic, quantitatively informed synthesis linking discovery trends to biological function and scalable production. In this review, we curate 71 reports of phosphonate natural products between 1959 and the present, primarily from bacterial sources, and analyze them across discovery modalities, bioactivity profiles, and producer taxonomy. We further summarize structure–activity relationships and consolidate engineering strategies—including metabolic engineering, synthetic biology, and biocatalytic cascades—employed to enhance phosphonate yields. Based on these analyses, we propose practical directions to accelerate the discovery of novel phosphonates, and improve their accessibility through advances in production and isolation technologies.