The COVID‐19 pandemic generated distinct mental health challenges, characterised by stress and anxiety due to its unpredictable duration and continuous threat. This study examined the role of meditation practice on anxiety symptoms and perceived stress, considering co‐variables such as self‐compassion, acceptance, awareness, brooding, lockdown duration, and sociodemographic characteristics. The study used a longitudinal design and data were collected through online surveys from April 2020 to January 2021 (at four different time points) and included 238 participants from Portugal (165 had prior experience with meditation practices, 73 were non‐meditators) with a mean age of 43.08 years (SD = 10.96). Linear mixed models revealed that over time, during the lockdown, the non‐meditators group demonstrated a greater increase of anxiety symptoms (β = −0.226, SE = 0.06, p = 0.006) and perceived stress (β = −0.20, SE = 0.06, p = 0.004), whereas the meditators group showed non‐significant (p > 0.05) variations in anxiety and stress symptoms during the same period of time. The effect of meditation on anxiety symptoms was moderated by sex, days of lockdown, self‐compassion, and acceptance. The effect of meditation on perceived stress was moderated by sex, years of education, days of lockdown, and levels of awareness. Additionally, the study explored the potential predictive effect of different meditation session lengths, indicating that longer meditation practices offered greater protection against an increase in anxiety symptoms. These findings highlight the importance of cultivating self‐regulation skills and investing in preventive mental health strategies to promote well‐being and autonomy. Mental health professionals should prioritise educating communities on evidence‐based practices like meditation and compassion exercises to enhance overall health.