Carboxylic acid-based natural deep eutectic solvents (CA-NADES), comprising acetic acid, citric acid, lactic acid, and malic acid as the hydrogen bond donors (HBD), and choline chloride as the hydrogen bond acceptor (HBA), were prepared at different molar ratios (1:1, 1:2, 1:3, 2:1, and 3:1). The viscosity and rheological properties of the CA-NADES were influenced by temperature, water content, molar ratios, the number of functional groups present in the carboxylic acid, and the state of the carboxylic acid at room temperature. The Fourier-transform infrared (FTIR) spectra of the various prepared NADES revealed the formation of new hydrogen bonds, and the structural features of the pure compounds were retained in the CA-NADES. In addition, the CA-NADES coupled with ultrasound-assisted extraction technique (UAE) were used for the extraction of bioactive compounds from date seed powder (DSP). The optimized parameters were molar ratio, extraction time, and solid-to-solvent ratio. The highest extraction efficiency of the CA-NADES was observed with carboxylic acid containing a single carboxylic acid functional group, in the order of lactic acid > acetic acid > citric acid > malic acid. Furthermore, DSP NADES-based extracts were stored under five different conditions (-20 °C, 4 °C, 37 °C, dark, and light). Similarly, freshly prepared CA-NADES were stored for 45 days to investigate any changes in physicochemical properties and extraction efficacy during the storage period. The result revealed that CA-NADES with multiple functional groups (citric and malic acid) retained more bioactive compounds (TPC) during the storage at −20 °C and 4 °C, and also maintained their extraction potentials compared to the CA-NADES with a single functional group. The outcomes of this study provided a broad understanding of the relationship between the physicochemical characteristics of the various CA-NADES, their storage stability, and extraction efficiency, which could be a useful tool for industrial applications.