Developing new nanomaterials and performing functionalization to increase their photocatalytic capacity are essential in developing low-cost, eco-friendly, and multipurpose-capacity catalysts. In this research, SnO2/Se-doped quantum dots (QDs) covered with glycerol (SnO2/Se-GLY) were synthesized using microwave irradiation. Then, their cover was replaced with glutaraldehyde through a ligand exchange procedure (SnO2/Se-GLUT). The XRD analyses confirmed a tetragonal rutile structure of SnO2. The HR-TEM analysis confirmed the generation of QDs with a size around 8 nm, and the optical analysis evidenced low bandgap energies of 3.25 and 3.26 eV for the SnO2/Se-GLY and SnO2/Se-GLUT QDs, respectively. Zeta-sizer analysis showed that the hydrodynamic sizes for both nanoparticles were around 230 nm (50 mg/L), and the zeta potential confirmed that SnO2/Se-GLUT QDs were more stable than SnO2/Se-GLY QDs. The cover-modified QDs (SnO2/Se-GLUT) showed a higher and faster adsorption capacity, followed by a slower photocatalytic process than the original QDs (SnO2/Se-GLY). The QTOF-LC-MS analysis confirmed MB degradation through the identification of intermediates such as azure A, azure B, azure C, and phenothiazine. Adsorption isotherm analysis indicated Langmuir model compliance, supporting the high monolayer adsorption capacity and efficiency of these QDs as adsorbent/photocatalytic agents for organic pollutant removal. This dual capability for adsorption and photodegradation, along with the demonstrated reusability, highlights the potential of SnO2/Se QDs in wastewater treatment and environmental remediation.