During biogas production anaerobic digestion of plant material produces a nutrient-rich residue called digestate. The application of the nutrients present in the digestate should improve soil fertility, particularly in nutrient poor soils, and thus crop yield, promoting the closure of the nutrient cycle. This study evaluated the effect of digestate application on the germination and early stages of plant development since these are the first steps to be considered when studying the benefits on plant growth in low fertility substrates. A greenhouse experiment was conducted to evaluate the effects of three substrates of different texture and fertility (field loam, field sand, sand), as well as type and amount of fertilizer (pure maize digestate vs. inorganic nitrogen/phosphorus/potassium (NPK) fertilizer) on both germination and early plant performance of maize (Zea mays L. subsp. mays). While digestate and NPK fertilizer applications had no significant effect on germination in the two field soils, digestate applications significantly decreased the germination rate in sand (36–82% reduction) due to an increase of surface water repellency. In contrast, for aboveground biomass yield, the most positive fertilization effects of digestate application were found on sand (up to 3.5 times the biomass of the unamended control) followed by field sand (1.5 times), compared to no effect for field loam. Our findings suggest that digestate application have positive fertilization effects in low-fertility substrates, similar to NPK, even though digestate application may have a negative impact on the permeability in sandy substrates that could interfere with germination.