Cyber attacks are growing with the rapid development and wide use of internet technology. Botnet attack emerged as one of the most harmful attacks. Botnet identification is becoming challenging due to the numerous attack vectors and the ongoing evolution of viruses. As the Internet of Things (IoT) technology is developing rapidly, many network devices have been subject to botnet attacks leading to substantial losses in different sectors. Botnets pose serious risks to network security and deep learning models have shown potential for efficiently identifying botnet activity from network traffic data. In this research, a botnet identification system is proposed based on the stacking of artificial neural network (ANN), convolutional neural network (CNN), long short-term memory (LSTM), and recurrent neural network (RNN) (ACLR). The experiments are conducted by employing both the individual models, as well as, the proposed ACLR model for performance comparison. The UNSW-NB15 dataset is used for botnet attacks and contains nine different attack types including 'Normal', 'Generic', 'Exploits', 'Fuzzers', 'DoS', 'Reconnaissance', 'Analysis', 'Backdoor', 'Shell code' and 'Worms'. Experimental results indicate the proposed ACLR model gains 0.9698 testing accuracy showing that it is successful in capturing the intricate patterns and characteristics of botnet attacks. The proposed ACLR model's k values (3, 5, 7, and 10) for a K-fold cross-validation accuracy score is 0.9749 indicating that the model's robustness and generalizability are demonstrated by k = 5. In addition, the proposed model detects botnets with a high receiver operating characteristic area under the curve (ROC-AUC) of 0.9934 and a precision-recall area under the curve (PR-AUC) of 0.9950. Performance comparison with existing state-of-the-art models further corroborates the superior performance of the proposed approach. The results of this research can be helpful against evolving threats and enhance cyber security procedures.