Crude glycerol (CG), an abundant by-product of bio-diesel production, has been identified as a suitable co-substrate for improving the biogas production of livestock manure through anaerobic digestion (AD). In this study, the potential of utilizing CG generated from the esterification of animal fats for biogas production was studied in both batch and continuous AD experiments, with emphasis on the importance of the hydraulic retention time (HRT). Batch experiments showed that the limiting step in the methane production rate during CG mono-digestion was the 1,3-propanediol uptake. Additionally, biochemical methane potential tests indicated that the addition of 1% w/w CG to swine manure-AD is more efficient in terms of percent of theoretical amount of methane obtained than the addition of 3% w/w. However, in continuous experiments, co-digestion of manure with 3% w/w CG did not exhibit any sign of inhibition within the HRTs tested (17–22 days). Moreover, a 222% increase of biogas productivity was observed with 3% CG supplementation at an HRT of 17 days, in contrast to a 146% increase at an HRT of 22 days. Based on this, and on the similar efficiency of soluble COD removal among the processes (ca. 93%), it was shown that it is possible to reduce the HRT without affecting negatively the efficiency of conversion of manure. Moreover, it was shown that CG from 2nd generation biodiesel based on animal fat, is a suitable feedstock for boosting the methane production of manure-based biogas plants.