Executive functions (EF) decline with age and this decline in older adults with generalised anxiety disorder (GAD) may be influenced by heart rate variability (HRV), brain-derived neurotrophic factor (BDNF), and physical fitness. Understanding these relationships is important for tailored treatments in this population. In this study, 51 adults with GAD (M age = 66.46, SD = 4.08) and 51 healthy controls (M age = 67.67, SD = 4.04) were assessed on cognitive inhibition (Stroop task), shifting (Trails part 4), flexibility (Wisconsin Card Sorting Test – Perseverative errors), working memory (Digit Span Backwards), IQ (Wechsler Abbreviated Scale of Intelligence), high frequency HRV, serum mature BDNF levels, and VO2 max. Results indicated that participants with GAD exhibited better cognitive inhibition compared to controls, with no general reduction in EF. Cognitive inhibition was predicted by gender, HRV, and BDNF levels, while cognitive shifting was predicted by gender and IQ, and cognitive flexibility and working memory by IQ. The enhanced cognitive inhibition in GAD participants might stem from maladaptive use of this function, characteristic of GAD, or protection from EF decline due to normal HRV. Increased BDNF levels, possibly due to good fitness, or compensatory mechanisms related to the disorder, might also play a role. These findings highlight the complexity of EF and related mechanisms in GAD, highlighting the need for interventions that consider both cognitive and physiological factors for optimal outcomes.