White matter hyperintensities (WMHs) are a risk factor for cognitive decline. Physical activity (PA) is associated with lower WMH. Whether long-term exposure to PA programs has beneficial effects on WMH progression in older adults with memory complaints and comorbid conditions has had limited exploration. This study explored whether a 24-month moderate-intensity PA intervention can delay the progression of WMH and hippocampus loss in older adults at risk for cognitive decline. Data acquired on magnetic resonance imaging were used to measure the progression of WMH and hippocampus loss. The results of this study showed no effect of intervention on either the primary outcome measure “WMH” or the secondary outcome measure “hippocampal volume.” In addition, neither beta amyloid status nor the adherence to the intervention had any effect on the outcome. In this cohort of subjective memory complaints and mild cognitive impairment participants with vascular risk factors, there was no effect of long-term moderate-intensity PA on WMH or hippocampal loss. •Results of a 24-month physical activity intervention in adults at risk of cognitive decline.•Minutes of physical activity per week was different between groups only at 6 months.•No intervention effect on primary outcome measure “white matter hyperintensities.”•Cognitive status or beta amyloid status did not affect outcome.•Secondary outcome measure “hippocampal volume loss” was not affected by intervention.