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Summary We present a spatially varying Robin interface condition for solving fluid‐structure interaction problems involving incompressible fluid flows and nonuniform flexible structures. Recent studies have shown that for uniform structures with constant material and geometric properties, a constant one‐parameter Robin interface condition can improve the stability and accuracy of partitioned numerical solution procedures. In this work, we generalize the parameter to a spatially varying function that depends on the structure's local material and geometric properties, without varying the exact solution of the coupled fluid‐structure system. We present an algorithm to implement the Robin interface condition in an embedded boundary method for coupling a projection‐based incompressible viscous flow solver with a nonlinear finite element structural solver. We demonstrate the numerical effects of the spatially varying Robin interface condition using two example problems: a simplified model problem featuring a nonuniform Euler‐Bernoulli beam interacting with an inviscid flow and a generalized Turek‐Hron problem featuring a nonuniform, highly flexible beam interacting with a viscous laminar flow. Both cases show that a spatially varying Robin interface condition can clearly improve numerical accuracy (by up to two orders of magnitude in one instance) for the same computational cost. Using the second example problem, we also demonstrate and compare two models for determining the local value of the combination function in the Robin interface condition.