The long-term effects of deforestation on tropical forest soil carbon reservoirs are important for estimating the consequences of land use on the global carbon cycle, but are poorly understood. The Maya Lowlands of Mexico and Guatemala provide a unique opportunity to assess this question, given the widespread deforestation by the ancient Maya that began ~4,000 years ago. Here, we compare radiocarbon ages of plant waxes and macrofossils in sediment cores from three lakes in the Maya Lowlands to record past changes in the mean soil transit time of plant waxes (MTTwax). MTTwax indicates the average age of plant waxes that are transported from soils to lake sediments, and comparison of radiocarbon data from soils and lake sediments within the same catchment indicates that MTTwax reflects the age of carbon in deep soils. All three sediment cores showed a decrease in MTTwax, ranging from 2,300 to 800 years, over the past 3,500 years. This decrease in MTTwax, indicating shorter storage times for carbon in lake catchment soils, is associated with evidence for ancient Maya deforestation. MTTwax never recovered to pre-deforestation values, despite subsequent reforestation, implying that current tropical deforestation will have long-lasting effects on soil carbon sinks.