The COVID-19 pandemic resulted in productivity losses, particularly for early career researchers (ECRs) who do not have the same track record as their non-ECR colleagues. Therefore, the purpose of the current study was to examine differences in time allocation and research productivity outcomes between ECRs and non-ECRs at a Carnegie Classification R1 University in the United States. We quantitatively and qualitatively examined differences in time allocation (i.e., research, teaching) and research productivity outcomes (e.g., peer-reviewed publications), as well as pandemic-related challenges, between ECRs and non-ECRs over three time periods: pre-pandemic, year one of the pandemic, and the first eight months of year two of the pandemic. Compared to non-ECRs, ECRs reported significantly more time spent on research, less time on teaching, fewer peer-reviewed publications, and fewer funding proposal submissions during the pandemic. Qualitative data revealed three broad categories of pandemic-related challenges: tangible (e.g., research delays), intangible (e.g., mental health), and long-term impacts on career trajectory (e.g., delayed promotion). The implications for future research and for universities looking to mitigate adverse impacts of the pandemic for ECRs are discussed.