Objective To achieve continuous production of fructooligosaccharides (FOS) by recycling of the mycelial cells containing the thermal-stable beta-fructofuranosidase in Aspergillus niger without immobilization. Results The thermal-stable beta-fructofuranosidase FopA-V1 was successfully expressed in A. niger ATCC 20611 under the control of the constitutive promoter PgpdA. The engineered A. niger strain FV1-11 produced the beta-fructofuranosidase with improved thermostability, which remained 91.2% of initial activity at 50 degrees C for 30 h. Then its mycelial beta-fructofuranosidase was recycled for the synthesis of FOS. It was found that the enzyme still had 79.3% of initial activity after being reused for six consecutive cycles, whereas only 62.3% beta-fructofuranosidase activity was detected in the parental strain ATCC 20611. Meanwhile, the FOS yield of FV1-11 after six consecutive cycles reached 57.1% (w/w), but only 51.0% FOS yield was detected in ATCC 20611. Conclusions The thermal-stable beta-fructofuranosidase produced by A. niger can be recycled to achieve continuous synthesis of FOS with high efficiency, providing a powerful and economical strategy for the industrial production of FOS.