Advances in material science dictate the search for sustainable options that target diverse applications that impact climate change. In this context, we report the exfoliation and expansion of g-C3N4 using PEI polymer, followed by gelation as beads using calcium alginate for adsorptive desulfurization of thiophene compounds. Adsorbent characteristics were exemplified through FT-IR, FE-SEM-EDX, TGA, XRD, BET-N2 isotherm, contact angle meter, XPS, HR-TEM, ZPC, and UTM. The PEI–g-C3N4 NSs@Ca-Alg bead composite with a mesoporous structure gave a specific surface area of 142.062 m2 g−1 yielding a high adsorption capacity of 183.03 mg S g−1. The material exhibited an ultimate tensile strength of 3500 kPa and a compressive stress of 527 kPa, accompanied by a compressive strain of 79%. The isotherm, kinetics, and thermodynamic investigations confirmed that the system exhibits pseudo-first-order kinetics and exothermic characteristics with spontaneity. The composite material had good potential for re-use for up to 5 adsorptive–desorption cycles with the potential to decrease the sulfur content to 58% in commercial diesel fuel.