Apart from the contaminant removal, the remediation of agricultural soil should also pay more attention to soil nutrient retention and biogeochemical cycling. This study aimed to evaluate changes of soil properties, potential nitrification rates (PNRs), and functional gene abundances and link their relationships after remediating co-contaminated agricultural soil with Medicago sativa L. (alfalfa) planting, alone or together with biochar application. Compared with the control (CK), alfalfa planting, alone or together with biochar application, could significantly increase soil organic matter (SOM) contents and discrepantly affect soil pH values. The PNRs of the amended treatments were significantly higher than that of the CK. Moreover, alfalfa plantings also enhanced the abundances of functional genes related to soil nitrification and denitrification, with the sole exception of nosZ gene. Stepwise regression analysis revealed that the PNRs were best described by the gene abundance ratios of AOB amoA/nifH and nirS gene abundances. Compared with the CK, alfalfa planting, alone or with biochar application, could restore nitrogen cycling in the co-contaminated agricultural soil and enhance the PNRs via decreasing contaminant bio-availabilities and increasing SOM contents and gene abundance ratios of AOB amoA/nifH.