There is growing interest for medicinal plants in the world drug market. Particularly, Matricaria recutita L., Valeriana officinalis L., Tilia spp., and Camellia sinensis (L.) Kuntze are some of the most consumed medicinal plants for treatment of minor health problems. Medicinal plants are seen as natural and safe; however, they can cause interactions and produce adverse reactions. Moreover, there is lack of consensus in medicinal plants regulation worldwide. DNA barcoding and UHPLC-MS technique are increasingly used to correctly identify medicinal plants and guarantee their quality and therapeutic safety. We analyzed 33 samples of valerian, linden, tea, and chamomile acquired in pharmacies, supermarkets, and herbal shops by DNA barcoding and UHPLC-MS. DNA barcoding, using matk as a barcode marker, revealed that CH1 sold as Camellia sinensis was Blepharocalyx tweediei, and sample TS2 sold as linden belong to Malvales. On the other hand, UHPLC-MS analysis revealed the presence of bioactive compounds (apigenin-7-glucoside, acetoxy valerenic acid, valerenic acid, epigallocatechin, and tiliroside). However, none of samples met minimum content of these active principles (except for valerenic acid in VF3) according to the European Medicines Agency (EMA) and Real Spanish Pharmacopeia. In conclusion, this study revealed the need to incorporate DNA barcoding and HPLC-MS techniques in quality controls of medicinal plants.