The Beaufort Sea region in the Canadian Arctic has undergone substantial sea ice loss in recent decades, primarily driven by anthropogenic climate warming. To place these changes within the context of natural climate variability, Holocene sea ice evolution and environmental conditions (sea surface temperature, salinity, terrestrial input) were reconstructed using lipid biomarkers (IP₂₅, and other HBIs, OH-GDGT, brGDGT, C_16:0 fatty acid, phytosterols) from two marine sediment cores collected from the Beaufort Shelf and slope, spanning the past 9.1 ka and 13.3 cal kyr BP, respectively. The Early Holocene (12–8.5 ka) is characterized by relatively higher sea surface temperature, lower salinity and no spring/summer sea ice until 8.5 ka on the Beaufort Sea slope. Around 8.5 ka, a peak in organic matter content is linked to both increased terrestrial input and primary production and may indicate increased riverine input from the Mackenzie River and terrestrial matter input from coastal erosion. Following this period, terrestrial inputs decreased throughout the Middle Holocene in both cores. A gradual increase in IP₂₅ and HBI-II concentrations aligns with relatively higher salinity, lower sea surface temperature and rising sea levels, and indicate the establishment of seasonal (spring) sea ice on the outer shelf around 7 ka and on the shelf around 5 ka. These patterns suggest an expansion of the sea ice cover beginning in the Middle Holocene, influenced by decreasing summer insolation. During the Late Holocene (4–1 ka), permanent sea ice conditions are inferred on the slope with a peak during the Little Ice Age. After 1 ka, seasonal sea ice conditions on the slope are observed again, alongside an increase in salinity and terrestrial input, and variable primary productivity. Similar patterns of Holocene sea ice variability have been observed across other Arctic marginal seas, highlighting a consistent response to external climate forcing. Continued warming may drive the Beaufort Sea toward predominantly ice-free conditions, resembling those inferred for the Early Holocene.