In this paper, citrus pomace was used as a source of pectin and polyphenols extracted in one pot solution by microwave-assisted extraction (MAE) and conventional extraction (CE) methods. MAE parameters were optimized to maximize yield and adjust in situ final physicochemical properties of extracted pectins, such as the methylation degree (DM), significantly influencing pectin functionality and application. Citric acid (CA) and acetic acid (Hac) were employed as solvents to mitigate pectin degradation. Extracted pectins were structurally (GPC and FTIR-ATR), morphologically (SEM), and thermally (TGA) characterized. From the reaction batch, the bioactive compounds (AOs) were separated and recovered, and their yield and antioxidant activities were evaluated with a DPPH assay. Moreover, by strategically selecting pH and solvents, this research enabled precise control over the final properties of pectin. The various characterization techniques employed show that the extraction conditions significantly influence the physicochemical and morphological properties of the material. Molecular weight (Mw) values range from 218 kDa to 567 kDa, surface morphology varies from compact/aggregated structures to three-dimensional network-like formations, and the DM spans from 34% (low DM) to 83% (high DM). This highlights a novel approach for predicting and tailoring in situ characteristics of extracted pectin to meet specific application requirements.