Fly ash (FA) and zeolite (Z) are known to reduce bioavailability of metals in soils via immobilization; however, these amendments may not only immobilize metals such as copper (Cu) and zinc (Zn), but also reduce nitrogen (N) and phosphorus (P) availability in the soils via sorption (for N by Z) and precipitation (for P by FA). This study was conducted to evaluate the effects of application of FA and Z (0, 5, and 10% rate) on the availability of nutrients as well as metals in the metal-contaminated soils cultivated with paddy rice (Oryza sativa L.). Both FA and Z reduced Cu and Zn uptake by rice while increasing metal retention in the soils regardless of the application rates. However, reduced uptake of metals did not translate into increase in rice growth, especially at the 10% of amendment rates, due to decreased nutrient uptake as indicated by higher NH4+ and available P concentration in the soils amended with Z and FA, respectively, which inhibited tillering in the early rice growth period and thus reduced biomass accumulation at maturity. Our results suggest that FA and Z may reduce Cu and Zn uptake by rice in the soils contaminated with the metals; however, the availability of N and P is likely to be co-decreased. We suggest that the capacities of FA and Z to immobilize nutrients as well as metals need to be considered prior to using the amendments in metal-contaminated rice paddies.