Among the species of the genus Crotalaria L., Crotalaria juncea is the only cover crop cultivated for its fiber. The quality of the latter depends on the nutritional conditions, accumulation of biophilic elements in the biomass, and synthesis of proteinogenic amino acids. Thus, the purpose of this study was a qualitative and quantitative assessment of the green harvest at the active flowering stage, before the bean formation phase, when the entire biochemical cycle of the plant is reconfigured, and the biochemical indicators are maximum. The plants were grown for 140 days (from April 22 to September 9, 2023) in protected soil conditions. The experimental design consisted of two units of 50 plants each: in the first (control) unit, plants were grown in a soil mixture without any additives; in the second one, they were treated three times during the growing season with an organic suspension of humic acids (1000 ppm) obtained from sapropel (Pskov oblast, UDHSS) by applying it when watering at the root. The soil substrate in both cases was typical chernozem (Kamennaya Steppe Nature Reserve, Voronezh oblast, 51°01′41.6″ N, 40°43′39.3″ E) with a 20% addition of volcanic zeolite. Over the course of every 14 days, morphometric trends of the crop growth (height and dry biomass) were systematically recorded with the removal of five cultivars from each unit of options. After 140 days, the remaining five replicates per option were subjected to biochemical analysis by inductively coupled plasma mass spectrometry (ICP-MS) and high-performance liquid chromatography (HPLC) using the 7500 and LC 1200 devices (Agilent Technologies, United States) according to the manufacturer’s method. Treatment with UDHSS increased productivity and shoot height by 51.1% and 11.3%, respectively. The microelement concentration order in the dry biomass was as follows: Na > K > Ca > S > P > Mg in the control option and Na > K > Ca > Mg > P > S in the UDHSS option, while the microelement export was observed as Fe > Mn > Zn > Ba > B > Cu > Mo and Fe > Mn > B > Zn > Ba > Cu > Mo. In total, the increase was more evident in the microelement accumulation due to a twofold increase in the concentration of iron ions. As for amino acids, L-lysine, L-glycine, L-glutamine, and L-tyrosine became higher. The first three are structural components of biological tissues indirectly indicative of an increase in the fiber strength of the plant culture.