Lentils are one of the most common legume crops used to diversify the cereal-oilseed cropping system in semi-arid environments. Lentils are a major source of protein and fiber for human consumption worldwide. However, the morphological characteristics of lentil plants—such as a short stem and low pod positioning—and complicated combine harvesting methods often result in yield loss. This also increases the susceptibility of a lentil crop to disease and render it less competitive against weeds. As a result, producers have resorted to using pesticides in order to mitigate the effects of weeds and disease. As a consequence, there have been undesirable negative environmental impacts on sustainable agroecosystems. Although land rolling, stubble management, and pesticide usage are common agronomic practices used to increase lentil yield and mitigate the issues associated with its morphology, their comprehensive effects on lentil growth and harvest loss are still not fully understood. In this study, we examined the impact of stubble management, the timing of land rolling, and the application of common fungicides and herbicides on lentil growth and yield. We found that stubble management and the timing of rolling modified lentil morphological structures, and thus impacted lentil yield and seed loss. These results were influenced by environmental factors, such as precipitation during the growing season. Although the results did not show significant interaction between fungicide application and lentil growth and yield, herbicide applications, stubble management, and the timing of rolling, along with common pesticide application strategies tested in our study, showed effects that were dependent on environmental conditions. Based on our results, we concluded that stubble management and the timing of rolling, combined with pesticide applications, can affect lentil seed loss and yield by modifying plant morphology. This was largely influenced by environmental conditions such as precipitation.