Soils in alpine mining areas suffer from severe heavy metal contamination and infertility, yet little is known about the effects of different materials on soil improvement in such regions. In this study, a field experiment was conducted in farmlands contaminated by the Lanping lead–zinc mine in Yunnan, China, to compare the effects of four materials (biochar, organic fertilizer, lime, and sepiolite) on soil properties, heavy metal (lead (Pb), cadmium (Cd), copper (Cu), and zinc (Zn) fractions and their availability, and the growth of Phaseolus coccineus L. Results showed that biochar and organic fertilizer significantly enhanced soil nutrient content and enzyme activities. Lime, biochar, and sepiolite effectively reduced heavy metal bioavailability by promoting their transition to residual fractions. Notably, biochar outperformed other materials by substantially increasing grain yield (by 82%), improving nutritional quality (sugars, protein, and starch contents raised by 20–88%), and reducing heavy metal accumulation in grains (by 36–50%). A comprehensive evaluation based on subordinate function values confirmed biochar as the most effective amendment. Structural equation modeling further revealed that biochar promoted plant growth and grain quality primarily by enhancing soil available nutrients and immobilizing heavy metals. These findings demonstrate the strong potential of biochar for remediating heavy metal-contaminated farmlands in alpine lead–zinc mining regions.