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The current study was conducted to estimate the carbon (C) storage status of agroforestry systems, via a non-destructive strategy. A total of 75 plots (0.405 ha each) were selected by adopting a lottery method of random sampling for C stock estimations for soil, trees and crops in the Mandi-Bahauddin district, Punjab, Pakistan. Results revealed that the existing number of trees in selected farm plots varied from 25 to 30 trees/ha. Total mean tree carbon stock ranged from 9.97 to 133 Mg C ha⁻¹, between 5–10 km away from the brick kilns in the study area. The decreasing order in terms of carbon storage potential of trees was <i>Eucalyptus camaldulensis</i> > <i>Syzygium cumin</i> > <i>Popolus ciliata</i> > <i>Acacia nilotica</i> > <i>Ziziphus manritiana</i> > <i>Citrus sinensis</i> > <i>Azadirachtta Indica</i> > <i>Delbergia sisso</i> > <i>Bambusa vulgaris</i> > <i>Melia azadarach</i> > <i>Morus alba</i>. Average soil carbon pools ranged from 10.3–12.5 Mg C ha⁻¹ in the study area. Meanwhile, maximum C stock for wheat (2.08 × 10⁶ Mg C) and rice (1.97 × 10⁶ Mg C) was recorded in the cultivated area of Tehsil Mandi-Bahauddin. The entire ecosystem of the study area had an estimated woody vegetation carbon stock of 68.5 Mg C ha⁻¹ and a soil carbon stock of 10.7 Mg C ha⁻¹. These results highlight that climate-smart agriculture has great potential to lock up more carbon and help in the reduction of CO₂ emissions to the atmosphere, and can be further used in planning policies for executing tree planting agendas on cultivated lands and for planning future carbon sequestration ventures in Pakistan.