Present study deals with evaluation of antibacterial activity of cinnamaldehyde and eugenol against both extended‐spectrum‐β‐lactamase (ESBL)‐producing and quinolone resistant (QR) (ESBL‐QR) pathogenic Enterobactericeae along with determination of its in vivo toxicity level in a murine model to investigate their pharmacological potential. Broth microdilution assay was used to determine minimum inhibitory concentrations (MICs) of cinnamaldehyde (CIN), eugenol (EG) and traditional antibiotics against ESBL‐QR Enterobactericeae. Sub‐acute oral toxicity study (14 days) was carried out in Swiss albino mice to evaluate any toxicological and behavioural effect viz novelty suppressed feeding (NSF), novel object recognition (NOR), tail suspension test (TST) and social interaction test of cinnamaldehyde and eugenol. Cinnamaldehyde and eugenol demonstrated mode‐MIC of 7.28 and 7.34 μg/mL among maximum numbers of Escherichia coli (32.1%) and 0.91 and 3.67 μg/mL among maximum numbers of Klebsiella pneumoniae (24.2%) isolates, respectively. For haematological and toxicological analyses, after 14 days of oral administration of cinnamaldehyde (0.91–10 mg/kg) and eugenol (7.34–70 mg/kg), blood was collected from the murine model, while histological examinations were performed on liver and kidney. There was no alteration in food and water intake among treated animals. Toxicological and behavioural studies displayed good safety profiles of cinnamaldehyde and eugenol. The results indicated potential antibacterial efficacy of cinnamaldehyde and eugenol against pathogenic ESBL‐QR Enterobacteriaceae, without any significant toxicological and behavioural effects.