Few randomized controlled trials investigated the effects of mindfulness intervention on older adults diagnosed with mild cognitive impairment (MCI). Furthermore, there have been hypotheses and theoretical mechanisms on the benefits of mindfulness intervention on biomarkers of stress, inflammation, and neuroplasticity implicated in MCI that warrant empirical evidence. We conducted a pilot randomized controlled trial to examine whether Mindful Awareness Practice (MAP) improved biomarker levels in older adults with MCI. Fifty-five community-dwelling older adults aged 60 and above were randomized into either the treatment arm, MAP, or the active control arm, the health education program (HEP). Researchers who were blinded to treatment allocation assessed the outcomes at baseline, 3-month, and 9-month follow-ups. Linear-mixed models were used to examine the effect of MAP on biomarker levels. MAP participants had significantly decreased high-sensitivity c-reactive protein (hs-CRP) levels at 9-month (β = -0.307, 95% CI = -0.559 to -0.054 P = 0.018). Exploratory sub-group analyses by sex showed significantly decreased hs-CRP in females only (β = -0.445, 95% CI = -0.700 to -0.189, P = 0.001), while stratification by MCI subtype showed hs-CRP decreased only in amnestic-MCI (aMCI) (β = -0.569, 95% CI = -1.000 to -0.133, P = 0.012). Although total sample analyses were not significant, males had significantly decreased interleukin (IL)-6 (β = -1.001, 95% CI = -1.761 to -0253, P = 0.011) and IL-1β (β = -0.607, 95% CI = -1.116 to -0.100, P = 0.021) levels at 3-month and non-significant improvements at 9-month time-point. MAP improved inflammatory biomarkers in sex- and MCI subtype-specific manners. These preliminary findings suggest the potential of mindfulness intervention as a self-directed and low-cost preventive intervention in improving pathophysiology implicated in MCI.