Intercropping is an eco-friendly approach for reducing weed problems through nonchemical methods. Intercrop effects on weed community structure have rarely been studied. A 6-yr study was initiated in 1999 and the response of aboveground weed flora (1999–2002 and 2005) and seed bank (2005) to the intercropping of saffron and black zira, two perennial crops was investigated. Mixtures consisted of 0/100, 25/75, 50/50, 75/25, and 100/0 saffron/black zira ratios, each planted at three densities: 30, 50, and 70 plant m⁻². The effect of planting density on weed populations was variable and in most cases not significant. However, mixture ratios caused drastic species compositional changes in the weed community for which univariate and multivariate analyses explored four major associations: (1) weeds that favored a higher ratio of saffron in mixtures (e.g., grasses, field bindweed, pigweeds), (2) weeds that preferred a higher ratio of black zira in mixtures (e.g., Persian speedwell, Brassicaceae complex, Polygoaceae complex, and earthsmoke), (3) weeds that were more abundant in 50/50 mixtures (e.g., Caryophyllaceae complex), and (4) weeds that showed no specific pattern (e.g., common lambsquarterss). Pigweeds, prostrate knotweed, and common lambsquarters dominated the viable seed bank with relative densities of 48, 28, and 8%, respectively. The seed bank of most weed species responded to mixture ratios in a similar manner to those of their corresponding aboveground flora. Seed density decreased as soil depth increased, leading to the accumulation of 66, 22, and 12% of viable seeds in soil layers of 0–5, 5–15 and 15–25 cm, respectively. Greater weed and seed densities were found in more pure stands of black zira. These findings contribute to improving current understanding of crop–weed community structures and may help in developing weed management practices.