A novel amine cross-linked magnetic biopolymer based on jute stick powder (AMB-JSP) was fabricated by in situ chemical co-precipitation method. The adsorbent AMB-JSP was applied to remove methylene blue (MeB) from aqueous solution. The adsorption efficiency of fresh jute sticks powder (JSP) and magnetic jute stick powder (MB-JSP) were also taken in consideration to build up a comparison study with the novel AMB-JSP adsorbent. The maximum MeB removals with AMB-JSP were observed as 85.71% at pH 8.0. Freundlich isotherm was best fitted for AMB-JSP while the Langmuir adsorption isotherm was suited for JSP and MB-JSP. The maximum MeB uptake for JSP, MB-JSP and AMB-JSP were found to be 157.23, 169.45 and 181.49 mgg− 1, respectively. The agitation times to reach equilibrium were found to be 160, 120 and 40 min for JSP, MB-JSP and AMB-JSP, respectively at temperature 303.15 K. The interparticle diffusion kinetics showed the best result for JSP, MB-JSP and AMB-JSP. In addition thermodynamic study indicated that the adsorption procedure was endothermic in nature and thus spontaneous. This study reveals that AMB-JSP could be applied as a potential magnetic bioadsorbent for the removal of MeB dye from an aqueous solution.