Organic acids (5% lactic acid and 5% acetic acid, w/v) and biosolvents (5% ethyl lactate, 5% and 10% d-limonene, w/v) are used as extraction agents during starch isolation from pea flour. NaOH at 0.4% w/v served as a control. The results show few differences in starch granular morphology, apparent amylose content, and most thermal parameters, and negligible differences in starch crystalline structure. However, noticeable differences are observed in protein and starch damage content, and pasting viscosities among starch isolated by different extraction agents. The starch extracted by 5% ethyl lactate has the highest protein residue (1.1%) compared to others (≤0.4%), while the starch extracted by 5% acetic acid shows the lowest pasting viscosities. d-Limonene at 5% seems to be a promising biosolvent to isolate pea starch for its low residual protein, and no solvent residue, yet the highest pasting viscosities in starch. Fourier transform infrared spectroscopy (FTIR) detects bands of residual protein in all samples, and also unique bands at 1564, 1575, and 1720 cm −1 related to acid residue in starches extracted by the two organic acids. Chemometric analysis of FTIR spectra differentiates starches extracted by biosolvents from those extracted by alkali and acidic agents.