Potential influence of management and handling procedures on alpacas’ behavioral and physiological responses has received little research attention so far and these are the first combined observations of alpacas' behavior with physiological stress assessment in Poland. Human influence on a farm animal can be measured by direct contact in neutral conditions and by an animal’s reactions during husbandry procedures. Quantifying the strength of the flight response toward approaching persons can help assess an individual’s suitability for use in various human–animal contact activities. Shearing is one of the potentially stressful husbandry procedures that can affect alpacas’ behavior and welfare. This study aimed to assess flight distance on the pasture and behavioral and physiological reactions during shearing in 34 alpacas. Two related questions have been raised: (1) do reactions to humans affect reactions to the shearing procedure? and (2) is shearing a stressful practice to alpacas based on both salivary cortisol and stress-related behavior? The flight distance toward humans (familiar and unfamiliar person) was measured. The stress reaction during shearing was assessed by behavioral observation and saliva sampling (to determine cortisol level). The animals that had a short flight distance to a familiar person also had a shorter flight distance to an unfamiliar one (P < 0.001). This study did not show that shorter flight distance to humans was connected with less intensive stress response during shearing. There was a difference (P < 0.001) between salivary cortisol levels before and after shearing, indicating that shearing is stressful for alpacas. It was observed that the later in order the animal was shorn, the fewer attempts to break free through abrupt movements were shown (P < 0.05). It was also noticed that the number of agonistic behaviors reduced as the shearing time increased (P < 0.05). Alpacas can adapt to stressful situations, and the animals most sensitive to stress should be shorn last.