<p>During the COVID-19 pandemic, organisations globally shifted into an emergency mode, leading to significant changes in the labour market. In light of these developments, this study sought to examine how the COVID-19 pandemic context influenced employees' evaluations of the different states of work motivation, as outlined in the framework of the Self-Determination Theory. A sample of 243 Portuguese employees completed the Multidimensional Work Motivation Scale (MWMS) at two-time points (before and during the pandemic). Repeated‐measures univariate and multivariate analyses of variance (MANOVA) were used to examine differences in work motivation scores between Time 1 and Time 2, as well to analyse the interaction between time and sociodemographic and work-related variables in the same dimensions. The results showed a positive and significant effect of the COVID-19 pandemic context on the more autonomous states of work motivation, i.e., Identified Regulation and Intrinsic Motivation, and those related to the controlled states of motivation, mainly Extrinsic Material Regulation and Introjected Regulation. In addition, workers without higher education have benefited more in terms of identified regulation throughout the pandemic, suggesting that the pandemic context may have facilitated the internalisation of new values and meaning at work for this group.This two-wave study suggests that the pandemic context acts as a psychological determinant affecting how job resources contribute to fulfilling autonomous motivation. The internal factors driving employees' autonomous motivation are shaped by their perception of the job resources within the wider context. In times of crisis, it is vital to focus on work resources and psychological needs to maintain employee motivation. Organisations must adjust their strategies to offer adequate support and balance demands and resources, especially during crises such as the pandemic.</p>