The present work reports the development of a new analytical method for the determination of free glycerol in biodiesel samples using enzymatic-spectrophotometric assay combined with solid phase extraction (SPE) by molecularly imprinted poly(methacrylic acid) (MIP). The spectrophotometric method was performed using a commercial enzyme kit. The enzymatic-spectrophotometric method showed good analytical performance in terms of the linearity (0.998), limit of detection (7.70 × 10−6% w/w), limit of quantification (2.54 × 10−5% w/w), repeatability (0.42% to 7.91%), and recovery (99.4% to 112%). The analyses of several biodiesel samples by SPE and enzymatic-spectrophotometric method provided recovery values between 91.4% and 105%. Therefore, the high selectivity of molecularly imprinted polymer (MIP) was successfully applied to isolate free glycerol from biodiesel samples containing acylglycerols and methyl esters, and thereby allow enzymatic-spectrophometric based quantification. The developed method using SPE with MIP was efficient for the determination of free glycerol in biodiesel and the obtained results are in agreement with gas chromatrography (GC) that was used as a reference protocol.