Production systems with woody perennial plants, ideally timber trees, are technologies accepted in carbon (C) projects to mitigate climate change. This research had as purpose the estimation of C storage and fixation in coffee production systems in Cundinamarca, Colombia. Carbon in biomass, necromass and soil were estimated in coffee plantations with three different shade levels (low, medium and high) in three municipalities using IPCC’s recommendations. Soil stored 75% of the total C (93.9 to 137.7 Mg C ha–1 in the upper 30 cm), followed by trees (19%). Carbon increases with a rise in shade (55.8 vs 42.0 vs 23.0 Mg C ha–1 for high, medium and low shade, respectively). These coffee plantations fixed a mean of 2.3 Mg C ha–1 year–1, with a maximum value of ~7.1 Mg CO ha–1 year–1 under a shade of 30% to 40%. Coffee plantations, especially with high shade, have a high potential of C fixation and mitigate climate change.