Male germ cells specifically express paralogues of components of the general transcription apparatus including ALF a paralogue of TFIIAα/β. We show that endogenous ALF is proteolytically cleaved to give α‐ and β‐subunits and we map the proteolytic cleavage site by mass spectrometry. Immunoprecipitations show that ALFα‐ and β‐subunits form a series of homologous and heterologous complexes with somatic TFIIA which is coexpressed in male germ cells. In addition, we show that ALF is coexpressed in late pachytene spermatocytes and in haploid round spermatids with transcription factor TRF2, and that these proteins form stable complexes in testis extracts. Our observations highlight how cleavage of ALF and coexpression with TFIIA and TRF2 increases the combinatorial possibilities for gene regulation at different developmental stages of spermatogenesis.