**Background:** Salvia hispanica L. (chia) is a plant from the Lamiaceae family traditionally used in nutrition and phytotherapy. While chia seeds are well-characterized and commercially important, other morphological parts of the plant — sprouts, leaves, flowers, roots, and herb — remain understudied. This study aimed to fill this gap by providing a comprehensive comparative analysis of the phytochemical composition, antioxidant capacity, and antimicrobial activity of extracts from seeds, sprouts, leaves, flowers, roots, and herb of S. hispanica.
**Methods:** Plant material was cultivated under greenhouse conditions at the Jagiellonian University Medical College, with seeds sourced from Guatemala. Hydromethanolic extracts (70% methanol) were prepared from freeze-dried plant tissues. Untargeted metabolomic profiling was performed using LC-Q-Orbitrap HRMS with negative ionization mode, coupled with Compound Discoverer software for data processing. Antioxidant profiling was conducted using HPLC-DAD with post-column derivatization using ABTS reagent, with antioxidant activity quantified as Trolox equivalents. Rosmarinic acid content was quantified by HPLC-DAD at 330 nm. Antimicrobial activity was assessed using the two-fold microdilution broth method against a panel of Gram-positive bacteria (Staphylococcus aureus ATCC 25923, S. aureus ATCC BAA-1707, Staphylococcus epidermidis ATCC 12228, Micrococcus luteus ATCC 10240, Bacillus cereus ATCC 10876), Gram-negative bacteria (Salmonella Typhimurium ATCC 14028, Escherichia coli ATCC 25922, Proteus mirabilis ATCC 12453, Klebsiella pneumoniae ATCC 13883, Pseudomonas aeruginosa ATCC 9027), and yeasts (Candida albicans ATCC 102231, Candida parapsilosis ATCC 22019, Candida glabrata ATCC 90030). MIC, MBC/MFC, and MBC/MIC index were determined.
**Key Results:** Metabolomic profiling identified 115 compounds across all extracts. The dominant compound class was terpenoids (31 compounds), followed by flavonoids (21 compounds), phenolic acids and derivatives (19 compounds), organic acids (16 compounds), and others including fatty acids and sugars. Organic and phenolic acids were the most abundant classes by total peak area. Rosmarinic acid was the main compound in all extracts, with the highest content in leaves (198.53 mg/100 g DW), followed by herb (185.12 mg/100 g DW), flowers (149.45 mg/100 g DW), sprouts (134.27 mg/100 g DW), and seeds (127.25 mg/100 g DW). Post-column derivatization with ABTS revealed that rosmarinic acid contributed 26–49% of total antioxidant activity across extracts: highest in sprouts (49.5%), herb (47.7%), and leaves (47.1%), and lowest in seeds (34.3%) and flowers (26.3%). Flower extracts showed the highest total antioxidant activity when expressed as Trolox equivalents. All extracts exhibited antibacterial and antifungal activity, with greater efficacy against Gram-positive bacteria. Gram-negative bacteria showed 4–8 times higher MIC values compared to Gram-positive bacteria. Leaf extracts demonstrated the strongest overall antibacterial activity, with bactericidal effects against S. aureus, S. epidermidis, M. luteus, and E. faecalis (MBC/MIC index = 1–4). The best antifungal activity against C. parapsilosis was observed for sprout extract (MIC = 0.625 mg/mL). Antibacterial efficiency ranked as: leaves > sprouts > whole seeds > ground seeds > roots > herb. Root extracts showed beneficial antifungal properties against C. parapsilosis and C. glabrata.
**Clinical Implications:** This study establishes that non-seed parts of S. hispanica, particularly leaves and sprouts, contain high levels of bioactive compounds with significant antioxidant and antimicrobial potential. The identification of rosmarinic acid as the primary contributor to antioxidant activity across all extracts supports its role as a key bioactive marker. The demonstrated antibacterial activity against clinically relevant Gram-positive pathogens and antifungal activity against Candida species suggests potential applications in infection management and food preservation. These findings may inform the development of novel plant-based antimicrobial agents and functional food ingredients, though the activity was substantially lower than standard antibiotics. Further research is needed to evaluate in vivo efficacy, safety, and optimal extraction methods for commercial applications.