BIOLOGICAL control of toxigenic fungi and their mycotoxins by using antagonistic bacteria has currently gained attention as a non-toxic replacement for harmful chemical substances. The present work aimed to study the inhibitory effects of five strains of bacteria recovered from soil on the growth of twenty isolates of Aspergillus niger obtained from Arabian coffee by using a dual-culture method and cell-free bacterial supernatant. Paraburkholderia fungorum and Bacillus subtilis were the two active strains used against three Aspergillus niger isolates with the highest inhibition percentage (86.81% and 62.97%, respectively). Biochemical tests partially identified the effective bacteria, and complete identification was confirmed by using the 16S rRNA sequence. P. fungorum and B. subtilis completely biodegraded the ochratoxins produced by A. niger-22 and A. niger-24, respectively. Interestingly, commercial amylase can suppressed ochratoxins biosynthesis by A. niger-28 with percentage of 44.7% using high-performance liquid chromatography (HPLC). A large number of bio-active compounds was detected in the bacterial filtrate by gas chromatography–mass spectroscopy (GC-MS). In vivo, the selected bacteria significantly biodegraded ochratoxins in contaminated grains using fluorometric method, with 52.9% as the highest inhibition percentage in maize contaminated by B. subtilis. This is the first report of ochratoxins biodegradation by P. fungorum and amylase.