Rhamnogalacturonan I (RG-I) is composed of a backbone of repeating disaccharide units →2)-α-L-Rhap-(1 → 4)-α-D-GalpA-(1→ with neutral sugar sidechains consisting of arabinose and galactose with variable linking types and chain lengths, corresponding to the hairy regions of pectin. This polysaccharide is abundant in the primary cell walls of fruits and vegetables. Biological functions of RG-I in immunomodulation and functional properties as a supplement and pharmaceutical expedient have increased commercial interest in RG-I extraction from fruit and vegetable waste. However, conventional extraction methods use harsh acid treatments that hydrolyze the side chains of RG-I. Innovative extraction technologies have been developed to preserve RG-I structure with better biological function. Therefore, the present review will focus on the influence of conventional and innovative methods exerts on the RG-I region of pectin from fruits and vegetables. Non-thermal processing (ultrasound, dielectric barrier discharge plasma, and enzymatic treatment) is superior to conventional and thermal processing (relying on high pressure, microwave and subcritical water extractions) in extracting branched RG-I from fruit and vegetables waste for food and pharmaceutical applications. Display omitted •RG-I is in the hairy region of pectin and has demonstrated biological functions.•Different extraction methods exert an influence on the final structure of pectin.•Harsh extraction conditions gives pectin rich in homogalacturonan but degrades RG-I.•Plasma/enzyme-assisted extraction or mild alkaline extraction gives RG-I pectins.•Combined non-thermal extraction gives pectins rich in neutral RG-I.