Bioproduction of 1,3-propanediol (1,3-PDO) is regarded as a low carbon footprint bioprocess with a 33% reduction of greenhouse gas (GHG) emissions compared to conventional chemical processes. In line with Sustainable Development Goal (SDG) 12, bioproduction of 1,3-PDO closes the loop between biodiesel waste glycerol and biobased 1,3-PDO to establish a circular bioeconomy. There are limited studies on the bioconversion of biodiesel-derived glycerol into 1,3-PDO via the immobilized cell biocatalysis route. In this study, the production of 1,3-PDO was enhanced by the wild-type Clostridium butyricum JKT 37 immobilized on the activated carbon of coconut shell (CSAC) as supporting material using the acidic-pretreated glycerol as a carbon source. Among various mesh sizes of CSAC tested, the 6-12 mesh immobilizer had enhanced cell density by about 94.43% compared to the suspended cell system. Following the acidic pretreatment in 37% (v/v) HCl, the pretreated glycerol had 85.60% glycerol with complete removal of soaps. The immobilized cell fermentation using pretreated glycerol produced 8.04 ± 0.34 g/L 1,3-PDO with 0.62 ± 0.02 mol/mol of yield, 15.81% and 27.78% higher than the control, respectively. Five repeated batches of immobilized cell fermentation had resulted in the average 1,3-PDO titer, yield, and productivity of 16.40 ± 0.58 g/L, 0.60 ± 0.03 mol/mol, and 0.68 ± 0.02 g/L.h, respectively. The metabolism pathway gradually shifted to a reductive branch when immobilized cells were reused in repeated batch fermentation, proven by the reduction in organic acid formation and the increased ratio of 1,3-PDO-to-total organic acids.