The modern analytical technique of Fourier-transform mid-infrared spectroscopy (FT-MIR) has found its place in routine wine quality control. It allows rapid and nondestructive analysis, with easy sample preparation and without the need for chemical pretreatment or expensive reagents. The objective of this research was to apply these advantages to fruit wines in order to create a tool for the authentication of fruit wines produced from different fruit species (chokeberry, blackberry, and raspberry). The aim of this work was to establish a chemometric model from FT-MIR spectra and to find a “fingerprint” of specific fruit wines, enabling the classification of fruit wines by plant species. Physicochemical analysis of 111 Croatian fruit wine samples (38 liqueur fruit wines and 73 fruit wines) revealed content levels of the following parameters: alcoholic strength (5.0–15.2% vol.), total dry extract (60.4–253.3 g/L), total sugars (1.2–229.9 g/L), pH (3.13–4.98), total acidity (4.2–18.3 g/L) and volatile acidity (0.2–1.5 g/L). For statistical data processing, spectral ranges between 926 and 1450 cm−1 and between 1801 and 2951 cm−1 were used. The first principal component (PC1) explained 70.4% of the observed variation, and the second component (PC2) explained 16.7%, clearly separating chokeberry fruit wines from blackberry and raspberry fruit wines. Soft Independent Modeling Class Analogy (SIMCA) was performed following the development of a PCA model showing that the chokeberry and blackberry wine samples form clearly separated clusters. Key discriminators for classifying chokeberry vs. blackberry wines were identified at 1157, 1304, and 1435 cm−1, demonstrating high discrimination power (DP 26, 17, and 14, respectively). FT-MIR spectroscopy, in combination with chemometric methods, has shown promising potential for the authenticity assessment of fruit wines.