It is generally recognized that agricultural soils accumulate toxic metals after long-term wastewater irrigation. The removal of trace metals (TMs) from the soil is not possible. Therefore, this study investigated the effects of manure amendments on the extractability and bioavailability of TM from the contaminated soil after wastewater irrigation. Soils samples were treated with co-composted cow manure (CM) and poultry litter (PL) at 10 and 20 t ha−1. The study showed that manure amendments enhanced fenugreek biomass and reduced TM uptake depending on the combination of composted manures used. TM concentrations in the fenugreek shoot varied in the order of Pb > Ni > Zn > Cu > Cd. A higher amount of manure mixture especially composted with the privet and cypress residues decreased the extractability of TM from the contaminated soil. Soils amended with PL reduced TM concentrations more than CM; this is also true for the plant uptake. The variation of TM in plants was positively associated with their concentrations in the soil and adversely related to the plant biomass. This study confirmed that the combined use of composted manure with plant residues can be an effective amendment for ameliorating the TM pollution in soils and crops.