Natural products, including honey, total alkaloids of Sophora alopecuroides (TASA) and matrine have been used in combination with antibiotics against various pathogenic bacteria. However, there are limited data on the antibacterial activity of these natural products in combination against multidrug‐resistant Pseudomonas aeruginosa strains. The in vitro activity of honey, TASA and matrine alone and in combination with antibiotics against P. aeruginosa isolates was investigated. In this study, four biofilm‐producing P. aeruginosa isolates, which were resistant to multiple antibiotics, were used. These natural products were not the most effective single agent against four isolates. The fractional inhibitory concentration index method revealed the synergistic effect of matrine and TASA‐honey in combination with ciprofloxacin (Cip) against all tested isolates. When these combinations were used, the resistance of isolates to Cip was decreased significantly (six to eightfold reduction in the minimum inhibitory concentration of Cip. The disk diffusion method showed that all isolates were resistant to β‐lactams. Combinations of these antibiotics with TASA and matrine changed slightly the activity of either antibiotic used as a single agent. All isolates produced metallo‐β‐lactamase enzymes (MBL). Pretreatment isolates with Cip‐matrine and Cip‐TASA‐honey resulted in a statistically downregulated expression of the mexA gene. These natural products can be used against overactivating MexAB‐OprM but not MBL‐producing P. aeruginosa isolates.