Yield monitoring systems in fruit production mostly rely on color features, making the discrimination of fruits challenging due to varying light conditions. The implementation of geometric and radiometric features in three-dimensional space (3D) analysis can alleviate such difficulties improving the fruit detection. In this study, a light detection and range (LiDAR) system was used to scan apple trees before (T
L) and after defoliation (T
D) four times during seasonal tree growth. An apple detection method based on calibrated apparent backscattered reflectance intensity (R
ToF) and geometric features, capturing linearity (L) and curvature (C) derived from the LiDAR 3D point cloud, is proposed. The iterative discretion of apple class from leaves and woody parts was obtained at R
ToF > 76.1%, L < 15.5%, and C > 73.2%. The position of fruit centers in T
L and in T
D was compared, showing a root mean square error (RMSE) of 5.7%. The diameter of apples estimated from the foliated trees was related to the reference values based on the perimeter of the fruits, revealing an adjusted coefficient of determination (R
2adj) of 0.95 and RMSE of 9.5% at DAFB
120. When comparing the results obtained on foliated and defoliated tree’s data, the estimated number of fruit’s on foliated trees at DAFB
42, DAFB
70, DAFB
104, and DAFB
120 88.6%, 85.4%, 88.5%, and 94.8% of the ground truth values, respectively. The algorithm resulted in maximum values of 88.2% precision, 91.0% recall, and 89.5 F1 score at DAFB
120. The results point to the high capacity of LiDAR variables [R
ToF, C, L] to localize fruit and estimate its size by means of remote sensing.
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