We evaluated the effect of the dog–owner relationship on dogs’ emotional reactivity, quantified with heart rate variability (HRV), behavioral changes, physical activity and dog owner interpretations. Twenty nine adult dogs encountered five different emotional situations (i.e., stroking, a feeding toy, separation from the owner, reunion with the owner, a sudden appearance of a novel object). The results showed that both negative and positive situations provoked signs of heightened arousal in dogs. During negative situations, owners’ ratings about the heightened emotional arousal correlated with lower HRV, higher physical activity and more behaviors that typically index arousal and fear. The three factors of The Monash Dog–Owner Relationship Scale (MDORS) were reflected in the dogs’ heart rate variability and behaviors: the Emotional Closeness factor was related to increased HRV (p = 0.009), suggesting this aspect is associated with the secure base effect, and the Shared Activities factor showed a trend toward lower HRV (p = 0.067) along with more owner-directed behaviors reflecting attachment related arousal. In contrast, the Perceived Costs factor was related to higher HRV (p = 0.009) along with less fear and less owner-directed behaviors, which may reflect the dog’s more independent personality. In conclusion, dogs’ emotional reactivity and the dog–owner relationship modulate each other, depending on the aspect of the relationship and dogs’ individual responsivity.