The contamination of arsenic (As) and cadmium (Cd) in paddy soils is widely reported and these two metals are difficult to be co-remediated due to the contrasting chemical behaviors. This poses a challenge to simultaneously decrease their availability in soil and accumulation in rice via immobilization by amendments, especially in in-situ fields. This study compared the effects of carbide slag, lodestone and biochar on the bioavailability of As and Cd in soil and their accumulation in rice tissues and root Fe–Mn plaque at tillering and mature stages in a paddy field. The addition of three amendments significantly limited the mobilization of As and Cd in soil and decreased their accumulations in brown rice by 30–52% and 9–21%, respectively. Carbide slag was most whereas lodestone least effective in As and Cd immobilization in the tested contaminated soils. Community Bureau of Reference (BCR) sequential extraction analysis showed that the amendments changed the forms of As and Cd to less-available. Activated functional groups of the amendments (e.g. –OH, C–O, OC–O, OH− and CO32−) sequestered metals by precipitation, adsorption, ion exchange or electrostatic attributes contributed greatly to the As and Cd immobilization in soil. Furthermore, the amendments promoted the formation of Fe–Mn plaque in rice roots, which further limited the mobility of As and Cd in soil and prevented their transport from soil to rice roots. The application of carbide slag and biochar but not lodestone increased rice yield compared to the unamended control, indicating their applicability in situ remediation. Our study gives a strong reference to select immobilizing amendments for food safe production in co-contaminated paddy soils. Display omitted •Amendments increased the soil pH from the tillering to mature stage.•Lodestone did not affect bioavailability and plant accumulation of Cd and As.•Carbide slag and biochar promoted the formation of Fe–Mn plaque.•Cadmium was more readily to be fixed in the Fe–Mn plaque than As.•Carbide slag and biochar worked well to decrease the accumulation of Cd and As in rice.