Natural non-allophanic Andosols often show aluminum (Al) toxicity to Al-sensitive plant roots. The significance of Al–humus complexes to Al toxicity has been emphasized. Allophanic Andosols also possess Al–humus complexes, but they rarely show any toxicity. In the present study, using model substances, we tested the toxicity of Al–humus complexes and its amelioration with allophanic materials. We extracted humic substances from the A horizons of a non-allophanic Andosol and an allophanic Andosol using a NaOH solution, and reacted the humic substances and partially neutralized AlCl3 solution at pH 4. Allophanic material was purified from commercial Kanuma pumice. Plant growth tests were conducted using a medium containing the Al–humus complexes (50 g kg−1), the allophanic material (0, 90, 180 and 360 g kg−1) and perlite. The root growth of barley (Hordeum vulgare L.) and burdock (Arctium lappa) was reduced in the media containing the Al–humus complexes derived from both the non-allophanic and allophanic Andosols when the allophanic material was not added. With the addition of the allophanic materials, particularly in the 360 g kg−1 treatment, the growth of the barley roots was improved markedly. Although the root growth of the burdock tended to improve with allophanic materials, the effect was weaker than that for barley. Monomeric Al in a solution of the medium was not detected (< 0.05 mg L−1) following the addition of 360 g kg−1 of allophanic materials, whereas 0.8–1.7 mg L−1 Al was recorded without the allophanic material.