Many experiments with juvenile trees require the non-destructive monitoring of plant biomass and growth which is most often conducted with allometric relationships between easy to measure morphological traits and plant biomass. In a growth experiment with potted juvenile Fagus sylvatica L. trees, we tested the practicability and accuracy of the portable 3D-laser scanner ZF Imager 5006 using the phase difference method for measuring total above-ground biomass (stems, twigs, leaves), the biomass of axes (stems and twigs), of leaves biomass and the leaf area of 63 experimental trees. The trees were scanned from 20 (or 21) different positions with an angular step width of 0.036° in horizontal and vertical direction and the 3D-point cloud of every tree was translated into a point cloud grid with defined distances between the data points to standardise the spatial resolution of the data. The validation of the laser scan data against traditional biomass harvest data gave good correlations for total above-ground biomass (green and woody plant material combined), leaf biomass and leaf area (obtained by measurements before and after leaf harvest), and the mass of stems and twigs (only woody compartments of the plants) with R 2-values between 0.61 and 0.88, all significant with p <0.001. Biomass estimates using allometric regressions between total plant height or total leaf number and above-ground biomass as alternative non-destructive methods were found to be weaker than laser scanning (R 2 0.54–0.67) and required a similar calibration effort. Repeated scanning of the same plant can be used to monitor biomass increase over time. We conclude that 3D-laser scanning is a promising technique for the non-destructive monitoring of biomass and growth in experiments with juvenile trees.