Multi-cropping is becoming an increasingly popular technique in agriculture to tackle major and complex agroecosystem problems such as biodiversity and soil fertility loss, erosion and degradation, increased greenhouse gas emissions, etc. Comprehensively assessing the impact of multi-cropping intensity on agroecosystems is a new and still under-researched approach that can provide a better understanding of the impact of individual indicators on the overall functioning of biodiverse agroecosystems. Data from a stationary field experiment using multi-cropping at the Vytautas Magnus University Experimental Station between 2020 and 2022 were used to carry out this study. The study included maize, hemp, and faba bean as single, binary, and ternary crops. A complex assessment approach (CEI value) was used to determine the impact of these crops on the agroecosystem, the interrelationships between the main indicators, and the strength of their effects. It was found that the ternary maize–hemp–faba bean crop had the most positive effect on the agroecosystem. The effectiveness of other crops was 2 to 35% less. The lowest value was calculated for the maize–faba bean crop.