Chitosan (CH)- and polycaprolactone (PCL)-based films containing nanocellulose (NC) (2% w/w) and grape seed extract (GSE) (15% w/w) were prepared in monolayer form (F1, F2, F5, F6) and bilayer form (F3, F4, F7, F8). Chicken breast fillets packaged with these films were analyzed for physicochemical (change in pH, color and thiobarbituric acid reactive substances-TBARS), and microbiological characteristics (total mesophilic aerobic bacteria (TMAB) and total coliform bacteria (TCB)) during 15 days under refrigerated conditions. The bilayer films with GSE kept the pH of the chicken breast fillets stable during storage. The resulting total color change (SE) was higher for the samples packaged with bilayer films, and chicken breast fillets packaged with bilayer films including GSE showed the highest SE values (p < 0.05). Samples packaged with GSE, and active bilayer films with GSE and NC had lower TBARS values than those of the control (p < 0.05). Film samples combined with GSE and NC led to a significant reduction in TMAB and TCB in chicken breast fillets (p < 0.05) during storage when compared with the control samples. The results indicated that CH-and PCL-based bilayer films could be a promising material to transfer functional compounds as active packaging material layers in food packaging applications.