Alcohol use disorder (AUD) is marked by sensitivity to alcohol cues and stress, increasing craving and stress. Stress typically lowers heart rate variability (HRV), whereas alcohol cues may increase or decrease HRV; however, their combined effects remain unclear. We examined (1) subjective craving, stress, and HRV responses to alcohol cue exposure and stress exposure, and (2) whether exposure order (stress–alcohol vs alcohol–stress) influenced these responses. Additional exploratory analyses examined associations between subjective and physiological reactivity. Fifty-six young adult who engaged in hazardous drinking (37 women; median age = 20 years, IQR = 3) with AUDIT scores ≥ 8 (median = 14, IQR = 6) and minimal other substance use were randomized to two conditions: stress–alcohol or alcohol–stress exposure. Alcohol cues included visual, olfactory, and tactile stimuli, and stress was induced using a computerized mental arithmetic task (MAT). Craving and stress were rated on Likert scales, and HRV was continuously recorded via a portable electroencephalograph (ECG) device. Alcohol cues increased craving. While stress exposure followed by alcohol cues reduced subjective stress. Alcohol cues increased HRV, while stress-exposure raised stress without affecting craving. In an exploratory subgroup analysis, HRV reactivity during MAT was observed only in participants whose craving remained unchanged change following MAT, suggesting an inverse association between craving and autonomic responsiveness. These findings highlight linked effects of stress exposure and alcohol cues on autonomic regulation in hazardous drinking and may offer preliminary insights into mechanisms that could be relevant for relapse prevention.