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Sex ratios are commonly skewed and variable in wild populations, but few studies track temporal trends in this demographic parameter. We examined variation in the operational sex ratio at two protected and declining breeding colonies of Magellanic Penguins (Spheniscus magellanicus) in Chubut, Argentina. Penguins from the two colonies, separated by 105 km, migrate north in the non-breeding season and have overlapping distributions at sea. Conditions during the non-breeding season can impact long-term trends in operational sex ratio (i.e., through sex-specific survival) and interannual variation in operational sex ratio (i.e., through sex-specific breeding decisions). We found an increasingly male-biased operational sex ratio at the two disparate colonies of Magellanic Penguins, which may contribute to continued population decline. We also found that the two colonies showed synchronous interannual variation in operational sex ratio, driven by variation in the number of females present each year. This pattern may be linked to sex-specific overwintering effects that cause females to skip breeding, i.e., to remain at sea rather than returning to the colony to breed, more often than males. Contrary to our predictions, colony-wide reproductive success was not lower in years with a more male-biased operational sex ratio. We did find that males showed more evidence of fighting and were less likely to pair when the operational sex ratio was more male biased. Our results highlight an indirect mechanism through which variation in the operational sex ratio can influence populations, through a higher incidence of fighting among the less abundant sex. Because biased sex ratios can reduce the size of the breeding population and influence rates of conflict, tracking operational sex ratio is critical for conservation., (© 2019 by the Ecological Society of America.)