Urban dwellers often breathe air that does not meet the European and WHO standards. Next to legislative initiatives to lower atmospheric pollutants, much research has been conducted on the potential of urban trees as mitigation tool for atmospheric particles. While leaf-deposited dust has shown to vary significantly throughout single tree crowns, this study evaluated the influence of micro-scale tree crown morphology (leaf density) on the amount of leaf-deposited dust. Using a ground-based LiDAR approach, the three-dimensional tree crown morphology was obtained and compared to gravimetric measurements of leaf-deposited dust within three different size fractions (>10, 3–10 and 0.2–3 µm). To our knowledge, this is the first application of ground-based LiDAR for comparison with gravimetric results of leaf-deposited particulate matter. Overall, an increasing leaf density appears to reduce leaf-deposition of atmospheric particles. This might be explained by a reduced wind velocity, suppressing turbulent deposition of atmospheric particles through impaction. Nevertheless, the effect of tree crown morphology on particulate deposition appears almost negligible (7% AIC decrease) compared to the influence of physical factors like height, azimuth and tree position.