Protein hydrolysates (PH) and humic substances (HS) are biostimulants that promote crop growth. Despite the widening of knowledge and insights provided by research activities over the past thirty years, there are still uncertainties concerning the possible direct absorption by plants of organic nitrogen as amino acids (AA) delivered as PH and the role of HS. This study aimed to assess the impact of PH treatment on the amino acid profile of maize seedlings and the influence of HS on amino acid uptake. Maize seedlings were treated with either PH from the yeast of the sugarcane fermentation process or a synthetic mixture of amino acids mimicking the PH composition using dual-labeled amino acids (13C, 15N glutamic acid) combined with commercially available humic substances. The amino acid profile was analyzed using HPLC, and plant tissues were examined for 15N using nuclear magnetic resonance (NMR) and mass spectrometry. The application of PH stimulated maize growth, with a more significant effect observed in the presence of humic substances. The treatments significantly altered the plants’ total amino acid content and composition profile. Maize seedlings actively uptake amino acids, representing 21% of the total nitrogen composition. The ascertained improvement of amino acid uptake stimulated by humic substances is associated with their effect on the differential expression of amino permease transporters and plasma membrane H+-ATPase. PH and amino acids enhance maize growth by significantly increasing amino acid uptake. The addition of humic substances further improved the biostimulant effects.