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In order to fully utilize the technological potential of unconventional superconductors, an enhanced understanding of the superconducting mechanism is necessary. In the best performing superconductors, the cuprates, superconductivity is intimately linked with magnetism, although the details of this coupling remain elusive. Here, we address this gap by studying the electron-doped cuprate Nd1.85Ce0.15CuO4−δ that has an antiferromagnetic ground state when synthesized and only becomes superconducting after a reductive annealing process. Using neutron spectroscopy, we show that the as-grown crystal exhibits a large spin pseudogap in the magnetic fluctuation spectrum. Annealing removes defects introduced by the commonly employed synthesis method and significantly reduces the spin pseudogap. While the spin pseudogap in the annealed sample likely arises from superconductivity, in the as-grown sample it results from the absence of long-wavelength spin waves. These results reveal a direct connection between defects, magnetism, and superconductivity, offering new insight into the mechanisms underlying high-temperature superconductivity and guiding the design of improved superconducting materials.