Medicinal and aromatic plants (MAPs) are gaining popularity globally as a source of raw materials for pharmaceuticals and traditional healthcare systems. More than 85% of herbal medicines used in traditional health care systems are derived from medicinal plants, ensuring millions of people's livelihoods, especially in the Indian Himalayan region (IHR). The wide altitudinal variation, different habitat conditions and varying microclimatic conditions in the Himalayan region form an ideal environment for the growth and development of MAPs. Therefore, the present study focused on standardization of propagation packages (seed germination) of two high-value medicinal herbs (Saussurea costus and Phytolacca acinosa) and analysis of morphological and physiological attributes in different growth conditions. Initially, different combinations and concentrations of PGRs (plant growth regulators) were used for the standardization of seed germination in targeted species. Results revealed the best seed germination for Saussurea costus in GA3 (250 µM) and GA3 (100 µM) for Phytolacca acinosa. These treatments reduced the mean germination time of targeted species, namely S. costus (95% germination with 14 days of MGT) and P. acinosa (80% germination with 11 days of MGT) and improved their germination percentage. After one year, seedlings were transferred to two different growth conditions (open field, and polyhouse) at Sri Narayan Ashram, Pithoragarh district (Altitude 2750 m asl), Uttarakhand for further analyzing the morphological and physiological attributes. Targeted species showed significant (p < 0.05) variation in both growth conditions and exhibited the best performance such as plant height (S. costus—138 cm; P. acinosa—145 cm), number of leaves (S. costus—22 ind; P. acinosa—93 ind), leaf length (S. costus—54.80 cm; P. acinosa—23.60 cm), leaf width (S. costus- 31.80 cm; P. acinosa—12.60 cm) and root length (S. costus—42.40 cm; P. acinosa—24.00 cm) in poly house. Similarly, physiological attributes were recorded significantly higher at poly house conditions like photosynthetic rate (S. costus—15.86 μmol m−2 s−1; P. acinosa—8.66 μmol m−2 s−1), stomatal conductance (S. costus—0.51 mol m−2 s−1; P. acinosa—0.28 mol m−2 s−1), leaf water potential (-0.23 MPa S. costus; -0.25 MPa P. acinosa), and maximal quantum efficiency of photosystem II (ratio Fv/Fm) (S. costus 0.82; P. acinosa 0.82). Furthermore, the analyzed parameters (morphological, physiological, and soil) showed a strong positive relationship. This study's finding revealed that Gibberelic acid concentration (250 µM; 100 µM) are best for seed germination. S. costus and P. acinosa showed higher growth performance and physiological responses at polyhouse conditions, which can be utilized for their large scale cultivation. Furthermore, quality plant materials (seeds, seedlings) can be used for commercial cultivation at barren/ agricultural land of the Indian Himalaya, to reduce pressure on natural resources and fulfill the market demands.