Agrobacterium-mediated transformation via floral inoculation (AMT-FI) enables genetic engineering without tissue culture. It is widely used in the model plant Arabidopsis thaliana, yet its efficiency and broader applicability remain limited. Here, we identify key floral stages and develop novel strategies to enhance AMT-FI-based genome editing. Using a dual-reporter system (RUBY and hygromycin resistance), we determined that flowers opened at 6 days post-inoculation (DPI) are optimal for high transformation efficiency, with nearly 100% of siliques harboring transformants. However, Agrobacterium infection induced ovule abortion, particularly in wild-type (Col-0) plants, whereas efr mutants lacking the EF-Tu receptor (EFR)-mediated pattern-triggered immunity (PTI) showed reduced ovule abortion. Notably, efr mutants exhibited more RUBY-positive ovules and significantly enhanced genome editing efficiency, despite showing no improvement in stable transformation rates. These results suggest that PTI restricts transient transformation rather than T-DNA integration. We further engineered stealth Agrobacterium strains expressing a chimeric EF-Tu for evading recognition by EFR. These GV3101-derived strains, named as AS201 and AS202, enhanced both transient transformation and genome editing efficiency without significantly altering stable transformation frequency. Remarkably, genome-edited T1 plants could be recovered based on phenotype or direct sequencing without the need for antibiotic selection when targeting flowers opened at 6 DPI. Our findings reveal EFR-mediated immunity as a key barrier to efficient transient transformation and genome editing via AMT-FI. By integrating floral stage selection, immune evasion, and Agrobacterium engineering, this study provides a practical and versatile platform to advance plant genome engineering.