This study presents the surface engineering and one-pot hydrothermal synthesis of a novel magnetic bio-heterostructure utilizing Spirulina biomass, MnFe2O4 nanoparticles, and N,S-doped carbonized polymer dots (N,S-CPDs) derived from agro-waste. Detailed surface characterizations, including XPS, TEM, FESEM-EDS, and VSM confirmed the robust interfacial integrity and superparamagnetic behavior of the composite. The Spirulina scaffold acts as a bio-template to prevent particle aggregation while providing abundant surface functional groups (hydroxyl, carboxyl, amine) that serve as “chemical hooks” for Arsenic(III) anchoring. Under visible-light irradiation, the Spr-algae@MnFe2O4/N,S-CPDs achieved 99.7% As(III) removal within 60 min. The reaction kinetics and residual arsenic concentrations were rigorously monitored using Microwave Plasma Atomic Emission Spectroscopy (MP-AES), ensuring high analytical sensitivity and precise validation of the degradation efficiency. Kinetic studies confirmed the process follows the Langmuir–Hinshelwood model (kapp = 0.012 min⁻1). The catalyst demonstrated excellent structural stability and magnetic recoverability, retaining > 91% efficiency after five cycles. This work provides atomic-level insights into the design of bio-interfaces for advanced remediation applications validated by high-precision spectrometry.