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The valorization of agro-industrial by-products has aroused great interest nowadays, due to their richness in phenolic compounds, including polyphenols, and their biological activities of high value for various areas. In this work, the recovery and concentration of these compounds, from hydroalcoholic extracts from hull and also blanching water, were studied, being two residues of large volume in the almond industry. The enrichment is given by sorption/desorption processes in columns packed with Molecularly Imprinted Polymers (MIPs), having used the polymers MIP-OA-3, MIPQUER-2 and MIP-QUER-3, and evaluating the enrichment efficiency against a gradient of several solvents in the elution steps. The hull extracts were obtained essentially by ultrasound, having worked with a hydroethanolic fraction 50/50 (v/v), due to their yield and equivalent favoring in the extraction of different polyphenolic families, being subsequently submitted to the sorption process. The characterization of the elutions of both by-products was mainly done by determining the total phenolic content (TPC) and the antioxidant activity by the DPPH method (EC50), and the best results were reinforced with chromatographic analyses by HPLC-DAD at 280 and 360 nm. The results show that the process allowed the selective fractionation and enrichment of phenolic compounds, observing fractions with a high degree of enrichment when compared to the initial extract, both at the TPC and EC50 levels. The intermediate hydroethanolic fractions, as well as the methanolic fractions, present the best results in terms of enrichment, as evidenced by the inverse relationship between TPC and EC50. It was also possible to verify differences in the enrichment trend between the OA3 column and the Q2 Q3 columns, revealing different affinities provided by the polymers. Chromatograms reveal significant changes in the chemical profile, both between fractions, extract and columns, suggesting and proving the enrichment of certain phenolic compounds, particularly flavonoids. In general, the results obtained indicate that the MIPs used have a high potential for phenolic enrichment from complex extracts, being able to fractionate and enrich, contributing to strategies for sustainable recovery of waste and development of processes aligned with the principles of green chemistry. Among these results, maximum TPC values of 615.66 ± 28.23 mg GAE/g Extract (hull) and 918.32 ± 34.54 mg GAE/g Extract (blanching water) were observed, together with EC50 values of 0.025 ± 0.000 and 0.028 ± 0.002 mg/mL, respectively. A value of 1135.64 ± 11.55 mg GAE/g Extract and 0.017 ± 0.000 mg/mL was also observed, indicating a high phenolic recovery.