Rising global concerns about global warming caused by pollution from excessive fossil fuels consumption, along with the high price of them in diesel engines, are the important reasons to search for fuels which is readily available and do not have destructive effects on the environment. Biodiesel is arguably the most appropriate and sustainable alternative to diesel fuel. Tomato seeds are one of the potential sources of biodiesel. They make up about 72% by weight of tomato waste, which contains an average of 24% oil. Tomato seed oil (TSO) can be used as a cheap and non-edible source of biodiesel. This paper investigated, both experimentally and numerically, the effects of different diesel–TSOB (tomato seed oil biodiesel) blends on the performance and emissions parameters of a four-cylinder, four-stroke, indirect injection diesel engine. The main goal of the paper was the simulation of the formation process of the emissions in the combustion chamber. The experimentally measured parameters such as torque, brake specific fuel consumption, exhaust gas temperature, nitrogen oxides, carbon monoxide, carbon dioxide, particulate matter, peak in-cylinder pressure, in-cylinder temperature and Reaction_Progress_Variable at different engine loads and speeds from 1200 to 2400 rpm at increments of 200 rpm are analyzed through ANOVA. The highest brake specific fuel consumption (BSFC) was observed for pure diesel and the lowest for the fuel blend with 10% biodiesel. The fuel blend with 20% biodiesel produced the highest torque. The engine was modeled using the AVL FIRE software. The model simulation results revealed that the highest nitrogen oxide (NOx) is produced in the throat of the combustion chamber to the top of the piston, the place of carbon dioxides (CO2) formation is near the combustion chamber boundaries and the location of carbon monoxides (CO) formation is near the combustion chamber boundaries and at the center area of the top of the piston. These results also show that the particulate matter (PM) emissions are formed where the fuel is injected into the combustion chamber.