Haloxylon persicum is a well-known plant of sandy deserts, but yet, its allelopathic and phytochemical potential has not been explored. In the present study, we evaluated the effects of different concentrations (1, 2, 4, and 8%) of the aqueous extract of H. persicum shoots on seed germination and seedling growth of wheat crop and black mustard weed. The effects of the same extract on the biochemical parameters (chlorophyll a, chlorophyll b, carbohydrates content, and proline content) of wheat seedlings were also investigated. Low and moderate concentrations (1, 2, and 4%) of H. persicum aqueous extract nonsignificantly affected seed germination, shoot length, root length, fresh weight, and dry weight of wheat seedlings, whereas these parameters were negatively affected by the application of the highest extract concentration (8%). The results revealed a significant increase in proline content in wheat seedlings under all the applied concentrations of H. persicum extract. Low and moderate concentrations (1–4%) of H. persicum extract significantly enhanced chlorophyll a, chlorophyll b, and total chlorophyll content in wheat seedlings, whereas these parameters were significantly reduced when the highest extract concentration (8%) was applied. Only the lowest concentration (1%) of H. persicum extract reduced the carbohydrates content of wheat seedlings, while other concentrations showed nonsignificant effects. Concentrations of 4 and 8% of H. persicum extract reduced the seed germination percentage of black mustard. The root length, shoot length, and fresh weight of black mustard seedlings were significantly decreased by the application of 1 and 2% extract concentrations and completely inhibited in response to treatment with 4 and 8% concentrations. The dry weight of black mustard seedlings was not affected by 1 and 2% extract concentrations but completely inhibited at 4 and 8% concentrations. The methanol extract of H. persicum contains high contents of bioactive secondary metabolites, such as phenolics, flavonoids, flavonols, anthocyanins, tannins, saponins, as well as proved to has a very strong antioxidant activity of the 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity (DPPH). Based on our results, we recommend the potential application of the aqueous extracts of H. persicum to control black mustard weed in wheat crops. Furthermore, H. persicum revealed an interesting phytochemical pattern with sound antioxidant activity that assigns this plant as a promising candidate to explore its detailed metabolomics profile along with potential bioactivities.