AbstractArctic organisms are adapted to the strong seasonality of environmental forcing. A small timing mismatch between biological processes and the environment could potentially have significant consequences for the entire food web. Climate warming causes shrinking ice coverage and earlier ice retreat in the Arctic, which is likely to change the timing of primary production. In this study, we test predictions on the interactions among sea ice phenology and production timing of ice algae and pelagic phytoplankton. We do so using the following (1) a synthesis of available satellite observation data; and (2) the application of a coupled ice‐ocean ecosystem model. The data and model results suggest that, over a large portion of the Arctic marginal seas, the timing variability in ice retreat at a specific location has a strong impact on the timing variability in pelagic phytoplankton peaks, but weak or no impact on the timing of ice‐algae peaks in those regions. The model predicts latitudinal and regional differences in the timing of ice algae biomass peak (varying from April to May) and the time lags between ice algae and pelagic phytoplankton peaks (varying from 45 to 90 days). The correlation between the time lag and ice retreat is significant in areas where ice retreat has no significant impact on ice‐algae peak timing, suggesting that changes in pelagic phytoplankton peak timing control the variability in time lags. Phenological variability in primary production is likely to have consequences for higher trophic levels, particularly for the zooplankton grazers, whose main food source is composed of the dually pulsed algae production of the Arctic.