The development of sustainable plant production systems involves a search for different alternatives to chemical fertilizers. The aim of the present study is to compare growth and physiological effects of vermicompost on Dracocephalum moldavica plants in controlled conditions, using two types of commercially available substrates. The intention is to determine whether nondestructively measured photosynthesis-related parameters are useful for monitoring the physiological status of plants. The plants were cultivated in two base substrates without or with the addition of mineral fertilizer, as well as an amendment with vermicompost at a 20% or 30% rate in the conditions of an automated greenhouse. The biomass accumulation for control plants of D. moldavica was identical in peat substrate and commercial garden soil. The average growth increase by mineral fertilizer was 25% for D. moldavica plants grown in peat and 15% for plants grown in soil. Substrate amendment with 20% vermicompost resulted in an 114% average increase in biomass for plants grown in peat and a 98% average increase for plants grown in soil, but for plants at 30% the amendment rate increase was 148% and 68%, for peat and soil, respectively. Consequently, the addition of an identical amount of vermicompost resulted in a poorer growth response of plants in commercial garden soil as a substrate in comparison to peat, but an increase in the amendment rate from 20% to 30% resulted in some growth inhibition for these plants. Chlorophyll concentration was positively affected by the vermicompost amendment in a concentration-dependent manner, but this effect during a cultivation period appeared relatively late. Large differences were found between the three groups of fluorescence-derived parameters, with variable levels of predictability with respect to the differences in plant yield due to the pronounced variation in correlation through time. It is concluded that the incorporation of vermicompost for the cultivation of D. moldavica, even in substrate mixes with relatively high and balanced composition of plant-available nutrients, benefits plant growth, physiological status and biomass yield, but it is necessary to explore interactions between vermicompost and other substrates leading to possible changes in quality-related characteristics of vermicompost in substrate mixes.