Nitrogen is an integral element of foliar sprays during apple fruit formation. However, in red cultivars, the application may have adverse effects on color in the second stage of fruit development. The effect of a low-dose foliar application of urea was monitored on ‘Topaz’ apple pomometric (fruit mass, firmness, total solids, starch content, skin color) and biochemical traits (primary metabolites, phenolic compounds, and assimilatory pigments). Three applications (17 July, 27 July, and 18 August) of two different urea doses (N1 = 1.4 kg N ha−1; N4 = 4 kg N ha−1) and control (N0, only sprayed with water) were used. Low doses of urea did not affect flesh firmness, total soluble, solid, and starch content, but individual fruit mass was significantly higher in N1 treatment compared to the other two treatments. Significantly lower a* parameters and a lower content of anthocyanins were measured on apples subject to N4 treatment. Many secondary metabolites (phenolic acids, flavan-3-ols, flavonols, and chalcones) were also negatively affected by low-dose urea application. Conversely, urea treatments significantly increased total assimilatory pigments in apple skin. Even minor levels of nitrogen, applied directly on the leaf at later stages of red apple fruit development, negatively altered color traits and the composition of metabolites.