In between January 2013 and January 2015, three chronic and complete SCI patients (thoracic level, flaccid paralysis) received 2 neural progenitor cells spinal cord implant and underwent intensive rehabilitation. During the evolution they showed recovery of electrical activity in muscles bellow the lesion level. Despite they continued the rehabilitation, muscular sings of severe atrophy persisted. In February 2016 and each 2 month they received intramuscular implant of muscular progenitor and neural progenitor cells looking forward to improve muscular trophism conditions in the muscles that had recovered the electrical activity. Three previously flaccid paraplegic patients received 6–8 intramuscular implants with autologous stem cells previously in vitro differentiated to muscular and neural progenitor cells. The implanted muscles had severe sings of denervation atrophy but had recovered electrical activity after spinal cord cell therapy. The muscular cell therapy was complemented with an intensive rehabilitation program. All implants were well tolerated, no signs of muscular damage were observed. Three out of 3 patients showed ultrasound and histological changes in the implanted muscles. Two out of 3 patients also recovered visible and palpable muscular contraction. One out of 3 recovered reflex activity. Although this is a preliminary study with a small population. The results show that intramuscular cell therapy combined with rehabilitation, may be a therapeutic option for histological and functional improvement in chronic denervated muscles that had previously recovered electrical activity.