Screening of microorganisms capable of producing the enzyme fructosyltransferase (FTase) that could be used for the production of fructooligosaccharides (FOS) led to the isolation of a strain of Aspergillus niger. The fungus produced extracellular FTase in both submerged fermentation (SmF) using chemically-defined medium, and solid state fermentation (SSF) using agricultural by-products such as kola nut pod and ripe plantain peel. Maximum enzyme activity of 24.49 Uml−1 was obtained in SmF after 48 h of fermentation, while maximum enzyme activities of 20.77 and 27.77 U g−1 were obtained in SSF using ripe plantain peel and kola nut pod, respectively. The enzyme was used to prepare fructooligosaccharides (FOS), with the maximum yield of 33.24% FOS, consisting of kestose and nystose produced by FTase of kola nut pod fermentation.The safety of prepared FOS was investigated using albino rats. The rats were grouped and fed orally with 2500 mg kg−1 bw/day of FOS, 5000 mg kg−1 bw/day FOS, 2500 mg kg−1 bw/day of honey and 2500 mg kg−1 bw/day of 60% sucrose, respectively, for a period of 30 days. Their effects on haemoglobin concentration, white blood cell count, differential count, blood glucose, protein, albumin, cholesterol, and histopathology of some organs were studied. The mean body weight (male rat) ranged between 161.80±22.37 to 196.00±16.50 g, while for female it ranged between 130.80±8.64 to 176.00±4.36 g. All haematological and blood chemistry parameters examined were normal, except for blood glucose which was higher in male/female rats fed with 60% sucrose. No histopathology changes were observed.From this study, it can be concluded that the studied strain of A. niger can utilize agro wastes, such as kola nut pod and ripe plantain peel for the production of FTase. The prepared FOS may be considered safe for consumption as alternative sweetener to sucrose, as it does not produce any pathological effect in the animals. It promoted good health in the experimental albino rat as seen in the haematology, blood chemistry and histopathology reports.