Lupins are an important source of domestic protein in many countries, and are often considered as an alternative to soybeans, given their elevated and high-quality protein content, suitability for sustainable production and consumer acceptability. The aim of the research was to determine the effect of the variety (indeterminate and determinate) and tillage system (conventional—CT, reduced tillage—RT, no-tillage—NT) on the chemical composition of three lupin species seeds (narrow leaved lupin—NL, yellow lupin—YL, white lupin—WL). The protein content of the lupin seeds ranged from 323 g kg−1 DM in the narrow-leaved lupin ‘Dalbor’ to 445 g kg−1 DM in the yellow lupin ‘Lord’. The tillage system significantly influenced the crude protein content only in NL seeds, with the greatest value observed with the NT system. An evaluation of the amino acid composition of the protein in the lupin seeds showed that the differences depended largely on the variation between the species. The conducted research shows that the varietal differentiation in terms of the amino acid content was particularly evident in NL and YL, and, to a lesser extent, in WL.