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Abstract Background Productivities of bioactive compounds in high-value herbs and medicinal plants are often compromised by uncontrollable environmental parameters. Recent advances in the development of plant factories with artificial lighting (PFAL) have led to improved qualitative and/or quantitative production of bioactive compounds in several medicinal plants. However, information concerning the effect of light qualities on plant pharmaceutical properties is limited. The influence of three different light-emitting diode (LED) spectra on leaf fresh weight (FW), bioactive compound production and bioactivity of Artemisia annua L. against the malarial parasite Plasmodium falciparum NF54 was investigated. Correlation between the A. annua metabolites and antimalarial activity of light-treated plant extracts were also determined. Results Artemisia annua plants grown under white and blue spectra that intersected at 445 nm exhibited higher leaf FW and increased amounts of artemisinin and artemisinic acid, with enhanced production of several terpenoids displaying a variety of pharmacological activities. Conversely, the red spectrum led to diminished production of bioactive compounds and a distinct metabolite profile compared with other wavelengths. Crude extracts obtained from white and blue spectral treatments exhibited 2 times higher anti-Plasmodium falciparum activity than those subjected to the red treatment. Highest bioactivity was 4 times greater than those obtained from greenhouse-grown plants. Hierarchical cluster analysis (HCA) revealed a strong correlation between levels of several terpenoids and antimalarial activity, suggesting that these compounds might be involved in increasing antimalarial activity. Conclusions Results demonstrated a strategy to overcome the limitation of A. annua cultivation in Bangkok, Thailand. A specific LED spectrum that operated in a PFAL system promoted the accumulation of some useful phytochemicals in A. annua, leading to increased antimalarial activity. Therefore, the application of PFAL with appropriate light spectra showed promise as an alternative method for industrial production of A. annua or other useful medicinal plants with minimal environmental influence.