The evolution of biogenic amines and other nitrogen compounds during the elaboration period of natural ciders in two successive seasons and two types of presses was studied. The harvest year affects the concentrations of most of the amino acids, while few of them were affected by the type of press. Asparagine and aspartic acid were the most abundant amino acids in fresh musts followed by α-alanine, α-aminobutyric acid, glutamine and glutamic acid. The mean concentrations of these amino acids in the fresh musts from the two harvest years were 12.35, 11.12, 6.45, 6.29, 5.28 and 4.87 mg L−1, respectively. During cidermaking, a decrease in the sum of all amino acids was detected (from 128 ± 54.311 mg L−1 to 22.5 ± 4.863 mg L−1 in 2005 and from 72.2 ± 15.256 mg L−1 to 6.5 ± 4.112 mg L−1 in 2006). Furthermore, significant differences in the concentration of most amino acids related to harvest year were observed. Concerning the biogenic amine content, putrescine was the main and the only amine present in all musts (3.72 ± 1.68 mg L−1) and ciders (3.59 ± 1.83 mg L−1). Histamine was the second biogenic amine of quantitative importance in final ciders (1.15 ± 0.69 mg L−1), and tyramine was only detected in one of the cidermaker cellars at the end of the elaboration period. The low concentrations of biogenic amines in ciders were attributed to the low contents of the corresponding precursor amino acids and do not affect to cider quality.