Handling is a crucial component of the human-horse relationship. Here, we report data from an experiment conducted to assess and compare the effect of two training methods. Two groups of six Welsh mares were trained during four sessions of 50 min, one handled with traditional exercises (halter leading, grooming/brushing, lifting feet, lunging and pseudo-saddling (using only girth and saddle pad) and the second group with natural horsemanship exercises (desensitization, yielding to body pressure, lunging and free-lunging). Emotional reactivity (ER) and the human-horse relationship (HHR) were assessed both prior to and following handling. A social isolation test, a neophobia test and a bridge test were used to assess ER. HHR was assessed through test of spontaneous approach to, and forced approach by, an unknown human. Horses' ER decreased after both types of handling as indicated by decreases in the occurrence of whinnying during stressful situations. Head movement (jerk/shake) was the most sensitive variable to handling type. In the spontaneous approach tests, horses in the traditional handling group showed higher latencies to approach a motionless person after handling than did the natural horsemanship group. Our study suggests that natural horsemanship exercises could be more efficient than traditional exercises for improving horses' HHR.