Nowadays most research in visual recognition using Convolutional Neural Networks (CNNs) follows the 'deeper model with deeper confidence' belief to gain a higher recognition accuracy. At the same time, deeper model brings heavier computation. On the other hand, for a large chunk of recognition challenges, a system can classify images correctly using simple models or so-called shallow networks. Moreover, the implementation of CNNs faces with the size, weight, and energy constraints on the embedded devices. In this paper, we implement the adaptive switching between shallow and deep networks to reach the highest throughput on a resource-constrained MPSoC with CPU and FPGA. To this end, we develop and present a novel architecture for the CNNs where a gate makes the decision whether using the deeper model is beneficial or not. Due to resource limitation on FPGA, the idea of partial reconfiguration has been used to accommodate deep CNNs on the FPGA resources. We report experimental results on CIFAR-10, CIFAR-100, and SVHN datasets to validate our approach. Using confidence metric as the decision making factor, only 69.8%, 71.8%, and 43.8% of the computation in the deepest network is done for CIFAR10, CIFAR-100, and SVHN while it can maintain the desired accuracy with the throughput of around 400 images per second for SVHN dataset. https://github.com/mfarhadi/AHCNN.