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The endophytic bacteria can be in symbiosis with host plants, owing to the natural stability advantages in degrading pollutants. To explore the technological feasibility of this method for indoor formaldehyde removal, a system combining endophytic bacteria and plants was established. In the present study, highly efficient formaldehyde-degrading bacteria Ochrobactrumintermedium, named strain ZH-1, was successfully induced with antibiotics (rifampicin) to an antibiotic-labeled strain ZH-1R without microbial variation. The strain ZH-1R was then used for colonization in the Epipremnum aureum and Chlorophytum comosumf. variegate plants by three inoculation methods: root irrigation (RI), acupuncture injury to stem (AS), and acupuncture injury to leaves (AL). The results demonstrated that the acupuncture injury to stem (AS) method was the most effective for inoculating ZH-1R strain in Epipremnum aureum plants. Conversely, acupuncture injury to stem (RI) method yielded the best results for the Chlorophytum comosumf. variegate plants, highlighting the importance of usage of optimal plant specific inoculation method ensuring the highest possible performance characteristics of the biological system. The results of 8-day formaldehyde dynamic fumigation experiment demonstrated that the removal efficiency of the formaldehyde by Chlorophytum comosum f. variegata inoculated with ZH-1R was significantly higher than the one demonstrated by non-inoculated plants. The average increase of 20.17% was observed during daytime, while much more significant improvement by 62.88% was achieved at night. This implied that endophytic bacteria could not only effectively improve the removal efficiency of formaldehyde, but also increased the resistance of not-native host plants to formaldehyde toxicity, suggesting its potential in an integrated system which provides a new path of an efficient and economical approach to radically improve indoor air quality, especially at nighttime.