Under the pro-environmental principles of agricultural production, soil cultivation and organic fertilization are of particular importance as strategical elements in reducing weed infestation in the context of sustainable agriculture. The aim of this study was to determine the effect of long-term practices that are used in regenerative agriculture (reducing soil tillage, cover crop management, and mineral nitrogen fertilization) on canopy weed infestation and the elements of spring barley architecture. Understanding the impact of the studied factors influences decision-making regarding weed infestation control, and thus may contribute to a reduction in herbicide use. A two-factor field experiment was conducted using the split-plot method. The main factors were four cultivation methods: 1. conventional tillage without a cover crop, 2. conventional tillage + cover crop, 3. reduced tillage + cover crop, and 4. no tillage + cover crop. The subplot factor was differentiated via nitrogen fertilization, at 40, 80, or 120 kg N∙ha−1. The research covered canopy weed infestation and the parameters of spring barley canopy architecture. The species composition; the number and weight of weeds; and, for barley, the leaf area index (LAI), density, length, and tillers were determined. The test results were statistically analyzed (ANOVA) in a series of experiments while using Tukey’s test for a significance level of p = 0.05. Additionally, simple linear regression analysis, principal component analysis (PCA), and data clustering (CA) were utilized. The study showed that simplified tillage contributed to reducing the number of weeds in the barley tillering stage, while also contributing to an increase in weed infestation during grain harvest. Plowing in the cover crop did not reduce the presence of undesirable plants in the canopy, while increasing doses of nitrogen fertilization contributed to a reduction in the number of weeds without affecting their mass. Weed infestation was also affected by meteorological conditions. Increased rainfall in the early stages of barley development benefits the number of weeds, especially in terms of traditional cultivation. Simplified tillage resulted in a reduction in barley density, height, and LAI, as well as an increase in the branching of the tested cereal. A significant negative correlation was also found between the weed infestation of the barley canopy and the characteristics of the canopy architecture. The PCA showed that the highest tillering of barley was provided at the lowest intensity of weed infestation. In turn, the CA indicated that the significantly higher LAI that resulted from a higher density and length of barley was attributed to the simplified cultivation treatments and the practice of direct sowing. It is a comprehensive method that can favor barley growth and development conditions while weakening weed infestation potential.