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Abstract PremiseAllopolyploidy—a hybridization‐induced whole‐genome duplication event—has been a major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. with their homoeolog in allopolyploids varies across taxa, and methods to detect homoeologous gene flow (HGF) are needed to understand how HGF has shaped polyploid lineages. MethodsThe ABBA‐BABA test represents a classic method for detecting introgression between closely related species, but here we developed a modified use of the ABBA‐BABA test to characterize the extent and direction of HGF in allotetraploidCoffea arabica. ResultsWe found that HGF is abundant in theC. arabicagenome, with both subgenomes serving as donors and recipients of variation. We also found that HGF is highly maternally biased in plastid‐targeted—but not mitochondrial‐targeted—genes, as would be expected if plastid–nuclear incompatibilities exist between the two parent species. DiscussionTogether, our analyses provide a simple framework for detecting HGF and new evidence consistent with selection favoring overwriting of paternally derived alleles by maternally derived alleles to ameliorate plastid–nuclear incompatibilities. Natural selection therefore appears to shape the direction and intensity of HGF in allopolyploid coffee, indicating that cytoplasmic inheritance has long‐term consequences for polyploid lineages.