Agroforestry practices that include the integration of multifunctional trees within agricultural lands can generate multiple socioecological benefits, in addition to being a natural climate solution due to the associated carbon sequestration potential. Such agroforestry trees represent a vital part of India’s landscapes. However, despite their importance, a current lack of robust monitoring mechanisms has contributed to an insufficient grasp of their distribution in relation to management practices, as well as their vulnerability to climate change and diseases. Here we map 0.6 billion farmland trees, excluding block plantations, in India and track them over the past decade. We show that around 11 ± 2% of the large trees (about 96 m² crown size) mapped in 2010/2011 had disappeared by 2018. Moreover, during the period 2018–2022, more than 5 million large farmland trees (about 67 m² crown size) have vanished, due partly to altered cultivation practices, where trees within fields are perceived as detrimental to crop yields. These observations are particularly unsettling given the current emphasis on agroforestry as a pivotal natural climate solution, playing a crucial role in both climate change adaptation and mitigation strategies, in addition to being important for supporting agricultural livelihoods and improving biodiversity.