Abstract Cross‐shelf interactions and the associated lateral transport of organic carbon remain poorly quantified and constrained by observations, despite their importance for the ocean carbon cycle. Filaments generated by instabilities of coastal currents are one pathway for this exchange, but their transport is difficult to observe at basin scales. Here, we provide the first satellite‐based estimate of offshore organic carbon transport and filament contribution in Eastern Boundary Upwelling Systems. Using a 21‐year (2003–2023) data set of chlorophyll‐a and sea surface temperature, we apply unsupervised k‐means clustering to detect offshore‐directed filaments and estimate their carbon content across isobaths of 250–2,000 m. We find an offshore transport of 239 ± 25 to 272 ± 28 TgC yr−1, with filaments contributing 8 ± 2 to 10 ± 3 TgC yr−1 (<5%). Filament transport shows a seasonal cycle linked to shelf carbon stock and mesoscale/submesoscale activity. Our results provide a scalable observational framework for monitoring lateral carbon transport.