Mitochondrial proteins of Plasmodium falciparum (MPPF) are an important target for anti-malarial drugs, but their identification through manual experimentation is costly, and in turn, their related drugs production by pharmaceutical institutions involves a prolonged time duration. Therefore, it is highly desirable for pharmaceutical companies to develop computationally automated and reliable approach to identify proteins precisely, resulting in appropriate drug production in a timely manner. In this direction, several computationally intelligent techniques are developed to extract local features from biological sequences using machine learning methods followed by various classifiers to discriminate the nature of proteins. Unfortunately, these techniques demonstrate poor performance while capturing contextual features from sequence patterns, yielding non-representative classifiers. In this paper, we proposed a sequence-based framework to extract deep and representative features that are trust-worthy for Plasmodium mitochondrial proteins identification. The backbone of the proposed framework is MPPF identification-net (MPPFI-Net), that is based on a convolutional neural network (CNN) with multilayer bi-directional long short-term memory (MBD-LSTM). MPPIF-Net inputs protein sequences, passes through various convolution and pooling layers to optimally extract learned features. We pass these features into our sequence learning mechanism, MBD-LSTM, that is particularly trained to classify them into their relevant classes. Our proposed model is experimentally evaluated on newly prepared dataset PF2095 and two existing benchmark datasets i.e., PF175 and MPD using the holdout method. The proposed method achieved 97.6%, 97.1%, and 99.5% testing accuracy on PF2095, PF175, and MPD datasets, respectively, which outperformed the state-of-the-art approaches.