Freeze-drying fresh vegetables and fruits may not only prevent post-harvest losses but also provide a concentrated source of nutrients and phytochemicals. This study focused on the phenolic composition of different freeze-dried products derived from horticultural crop remains (HCRs) in the vegetable and fruit production chain. These products may be considered as a potential health-promoting solution for preventing post-harvest fruit spoiling and losses. The total polyphenolic content (TPC) and the main phenolics were studied using high-performance liquid chromatography (HPLC) with a diode array detector (DAD). Additionally, an in vitro chemical screening of the antioxidant capacity was carried out using the Ferric Reducing Antioxidant Power (FRAP) assay. These analyses were performed together with an investigation of the correlations among phenolics and their antioxidant properties, and a bioinformatic approach was used to estimate the main potential bio-targets in human beings. Furthermore, a statistical approach using Principal Component Analysis (PCA) was carried out for a multivariate characterization of these products. Catechins, flavonols, and phenolic acids were the predominant and most discriminating classes in different products. The TPC values obtained in this study ranged from 366.86 ± 71.30 mg GAE/100 g DW (apple, MD) to 1077.13 ± 35.47 mg GAE/100 g DW (blueberry, MID) and 1102.25 ± 219.71 mg GAE/100 g DW (kaki, KD). The FRAP values ranged from 49.28 ± 2.88 mmol Fe/kg DW (apple, MD) to 80.43 ± 0.02 mmol Fe/kg DW (blueberry, MID) and 79.05 ± 0.21 mmol Fe/kg DW (kaki, KD). The proposed approach may be an effective tool for quality control and valorization of these products. This study showed that the utilization of crop remains can potentially lead to the development of new functional foods, providing additional economic benefits for farmers. Finally, the use of freeze-drying may potentially be a sustainable and beneficial solution for growers who may directly utilize this technology to produce dried products from the crop remains of their fruit productions.