The use of small, maneuverable, untethered and reconfigurable robots could provide numerous advantages in various micromanipulation tasks. Examples include microassembly, pick-and-place of fragile microobjects for lab-on-a-chip applications, assisted hatching for in-vitro fertilization and minimally invasive surgery. This study assesses the potential of soft untethered magnetic grippers as alternatives or complements to conventional tethered or rigid micromanipulators. We demonstrate closed-loop control of untethered grippers and automated pick-and-place of biological material on porcine tissue in an unstructured environment. We also demonstrate the ability of the soft grippers to recognize and sort non-biological micro-scale objects. The fully autonomous nature of the experiments is made possible by the integration of planning and decision-making algorithms, as well as by closed-loop temperature and electromagnetic motion control. The grippers are capable of completing pick-and-place tasks of biological material at an average velocity of 1.8±0.71 mm/s and a drop-off error of 0.62±0.22 mm. Color-sensitive sorting of three micro-scale objects is completed at a velocity of 1.21±0.68 mm/s and a drop-off error of 0.85±0.41 mm. Our findings suggest that improved autonomous un-tethered grippers could augment the capabilities of current soft-robotic instruments especially in advanced tasks involving manipulation.