Packaging plays a key role in preserving food products during transportation. Therefore, selecting proper packaging crates to transport fruits from farms to the market can dramatically reduce loss and waste. This study aims to evaluate the environmental impact of two packaging alternatives when transporting citrus products in Jordan using the loss ratio, as an indicator to select the best packaging, based on the traveled distances. The research team tracked transportation trucks from several farms to the market. In addition, data were collected from the department of statistics in Jordan to build the model using OpenLCA Software with defined system boundaries. However, the results revealed that polypropylene crates performed better than polystyrene crates. Citrus loss during transportation was cut by at least 60% when using polypropylene crates. The use of polypropylene crates reduced product damages by handling better the vibration and load stress, especially with increased transport distances to the “Central Market of fruits and vegetables”. Different impact categories were evaluated. We selected 3 categories based on the hotspot analysis performed: climate change, resource depletion, and water resource depletion. Farm waste has the highest impact with ranges of 58–69%, 77–85%, and 77–81%, respectively. Other impactful waste is waste from packaging and inedible parts; they influence the impact categories up to 23%, 11%, and 17%, in the same order. In terms of environmental impact, the polypropylene crates have fewer impacts since they are reusable and recyclable at the end of the product life cycle. Therefore, we recommend adopting polypropylene crates when transporting citrus products to the market. As a future research direction, the study suggests performing a similar analysis to evaluate the effect of packaging crates on other agricultural products in Jordan.