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As cities transform, debates have centered on the degree to which gentrification spatially reorganizes and exacerbates racial and class inequality. This study examines how gentrification is associated with the structure of segregation from 1990–2010 across 100 metropolitan areas. Using data from the US Census and the American Community Survey and a new decomposition approach for measuring segregation, we examine how the prevalence of gentrification across cities are associated with changes in segregation for racial and ethnic groups by socioeconomic status and the degree to which this is occurring between and within central cities and suburbs across metropolitan areas. While gentrification is associated with overall decreases in income segregation, it differentially affects segregation levels of poor residents by racial and ethnic groups and differentially across central cities and suburbs. The results demonstrate how contemporary urban changes simultaneously integrate some groups in some places yet further segregate others.