There are great interests in developing speech recognition using deep learning technologies due to their capability to model the complexity of pronunciations, syntax, and language rules of speech data better than the traditional hidden Markov model (HMM) do. But, the availability of large amount of data is necessary for deep learning-based speech recognition to be effective. While this is not a problem for mainstream languages such as English or Chinese, this is not the case for non-mainstream languages such as Indonesian. To overcome this limitation, we present deep features based on convolutional neural networks (CNN) for Indonesian large vocabulary continuous speech recognition in this paper. The CNN is trained discriminatively which is different from usual deep learning implementations where the networks are trained generatively. Our evaluations show that the proposed method on Indonesian speech data achieves 7.26% and 9.01% error reduction rates over the state-of-the-art deep belief networks-deep neural networks (DBN-DNN) for large vocabulary continuous speech recognition (LVCSR), with Mel frequency cepstral coefficients (MFCC) and filterbank (FBANK) used as features, respectively. An error reduction rate of 6.13% is achieved compared to CNN-DNN with generative training.