This study investigates the use of graphene oxide (GO) nanocarriers functionalized with polyethylene glycol (PEG), polyethyleneimine (PEI), and chitosan (CS) for the delivery of the Clustered Regularly Interspaced Short Palindromic Repeats-associated protein 9 (CRISPR-Cas9) complex in plant systems. GO-polymer conjugates were synthesized and characterized for surface charge and Cas9 protein loading efficiency. Results showed that positively charged GO-PEI conjugates exhibited superior Cas9 loading, effectively incorporating GFP (Green fluorescent protein) tagged Cas9 proteins into plant cells. To assess the biological effects of GO-PEI nanocarriers, RNA sequencing (RNA-seq) data from Arabidopsis thaliana (GSE172278) treated with PEI-functionalized single-walled carbon nanotubes (SWNTs), SWNTs with single-stranded RNA, water, and untreated controls were analyzed. Differential expression analysis identified stress-responsive candidate genes, and the responses of selected stress markers in Arabidopsis thaliana seedlings treated with GO-PEI nanocarriers were investigated via quantitative PCR (qPCR). The biocompatibility and effectiveness of GO as a gene delivery platform were shown by comparing the expression of stress genes in systems treated with GO with those based on carbon nanotubes (CNTs). The results show that GO-based nanocarriers are a potential approach for effective plant genome editing, especially those functionalized with cationic polymers like PEI. This strategy could speed up sustainable developments in agricultural biotechnology and improve crop resilience.