The objective of this study is to assess the associations of race/ethnicity and severe housing problems with COVID-19 death rates in the US throughout the first three waves of the COVID-19 pandemic in the US. We conducted a cross-sectional study using a negative binomial regression model to estimate factors associated with COVID-19 deaths in 3063 US counties between March 2020 and July 2021 by wave and pooled across all three waves. In Wave 1, counties with larger percentages of Black, Hispanic, American Indian and Alaska Native (AIAN), and Asian American and Pacific Islander (AAPI) residents experienced a greater risk of deaths per 100,000 residents of +22.82 (95% CI 15.09, 30.56), +7.50 (95% CI 1.74, 13.26), +13.52 (95% CI 8.07, 18.98), and +5.02 (95% CI 0.92, 9.12), respectively, relative to counties with larger White populations. By Wave 3, however, the mortality gap declined considerably in counties with large Black, AIAN and AAPI populations: +10.38 (95% CI 4.44, 16.32), +7.14 (95% CI 1.14, 13.15), and +3.72 (95% CI 0.81, 6.63), respectively. In contrast, the gap increased for counties with a large Hispanic population: +13 (95% CI 8.81, 17.20). Housing problems were an important predictor of COVID-19 deaths. However, while housing problems were associated with increased COVID-19 mortality in Wave 1, by Wave 3, they contributed to magnified mortality in counties with large racial/ethnic minority groups. Our study revealed that focusing on a wave-by-wave analysis is critical to better understand how the associations of race/ethnicity and housing conditions with deaths evolved throughout the first three COVID-19 waves in the US. COVID-19 mortality initially took hold in areas characterized by large racial/ethnic minority populations and poor housing conditions. Over time, as the virus spread to predominantly White counties, these disparities decreased substantially but remained sizable.