Aluminum (Al) is biotoxic, often active in acid soil and retards the growth of crop roots. Cayenne is a type of pineapple cultivar that can be well cultivated in a strongly acid environment containing AlCl3 concentrations up to 300 μmol L−1. In addition to organic acids, variations in the proteins in root apices are regarded as the mechanism involved in Al resistance. The objective of the present study was to explore the responsive proteins of Al stress in a known Al-resistant pineapple cultivar (i.e. Cayenne). After root emergence, pineapple seedlings were exposed to hydroponic solutions each containing 0 and 300 μmol L−1 AlCl3 for 4 weeks. The total proteins in the root apices were separated using 2-D electrophoresis and a total of 17 apparently differential spots were identified by mass spectrometry, with 10 upregulated and seven downregulated proteins. The root apices of Cayenne under Al stress could be characterized by cellular activities involved in, for example, carbohydrate metabolism, organic acid production, energy metabolism, alleviating redox damage and root phenotypical change, which are critical for plant survival under Al toxicity. In contrast, there are one hypothetical and three unknown proteins that play unknown roles in Al resistance and warrant further investigation. The present study may provide an important clue to future proteomic research on Al-resistant mechanisms in pineapple.