The root apical meristem (RAM) is maintained by a complex network of transcription factors and phytohormones, the main one being auxin. PIN-FORMED (PIN) transporters maintain auxin distribution within the meristem and are important for its patterning. Severe damage to the RAM, such as complete excision of its distal part, triggers auxin-mediated regeneration by rapid formation of a new stem cell niche. To test the role of directed auxin transport during this process, we used genetic and chemical perturbations of PIN-mediate transport, and show that, surprisingly, disruption of auxin transport did not inhibit regeneration or the activation of auxin response near the injury site. In contrast, inhibition of auxin biosynthesis resulted in complete abortion of regeneration. Using chemical inhibition and tissue specific expression of an artificial miRNA targeting auxin biosynthesis enzymes, we show that multiple local auxin sources, acting in temporal succession, are required for cell cycle activation and for proper meristem patterning throughout the regeneration process. Finally, we show that roots that not accumulate auxin at the regeneration site cannot regeneration, but restoration of auxin supply to these roots resulted in recovery of regeneration. We suggest that localized biosynthesis, and not transport, is the key regulator of auxin distribution during regeneration and that the ability to specify new auxin sources is one of the cardinal features enabling plant regeneration.