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We consider a continuous-time model describing the interaction between phytoplankton and zooplankton using a Holling type-II response. We then transform this continuous-time model into a discrete-time counterpart using a fractional-order discretization method. The paper explores the local stability of this obtained system concerning all equilibrium points and establishes the global asymptotic stability of its positive fixed point. The study also demonstrates that, under specific mathematical conditions, the system undergoes a Neimark–Sacker bifurcation around its positive equilibrium point. To effectively manage this bifurcation, two modified hybrid control techniques are introduced. The paper concludes by presenting illustrative numerical examples that validate the theoretical findings and assess the effectiveness and feasibility of the newly proposed control strategies. In addition, a comparative analysis is conducted between the modified hybrid techniques and an existing hybrid approach.