The invention relates to a method and system for picking up and collecting plant matter, in particular plant embryos. To pick up the plant matter, a pick-up unit is used that is mounted to a robotic arm. According to the invention, two separate imaging steps are performed at two different positions of the pick-up unit. The first imaging step is performed to identify an isolated piece of plant matter. The second imaging step is performed when the pick-up unit is at a confirming position and enables a verification of whether a piece of plant matter has been picked up or not. The confirming position is in between the position of the pick-up unit for picking up plant matter and the position for depositing plant matter in suitable receptacles.