Convolutional neural networks have remarkably progressed the performance of distinguishing plant diseases, severity grading, and nutrition deficiency prediction using leaf images. However, these tasks become more challenging in a realistic in-situ field condition. Often, a traditional machine learning model may fail to capture and interpret discriminative characteristics of plant health, growth and diseases due to subtle variations within leaf subcategories. A few deep learning methods have used additional preprocessing stages or network modules to address the problem, whereas several other methods have utilized pre-trained backbone CNNs, most of which are computationally intensive. Therefore, to address the challenge, we propose a lightweight autoencoder using separable convolutional layers in its encoder decoder blocks. A sigmoid gating is applied for refining the prowess of the encoders feature discriminability, which is improved further by the decoder. Finally, the feature maps of the encoder decoder are combined for rich feature representation before classification. The proposed Convolutional Lightweight Autoencoder for Plant disease classification, called CLAP, has been experimented on three public plant datasets consisting of cassava, tomato, maize, groundnut, grapes, etc. for determining plant health conditions. The CLAP has attained improved or competitive accuracies on the Integrated Plant Disease, Groundnut, and CCMT datasets balancing a tradeoff between the performance, and little computational cost requiring 5 million parameters. The training time is 20 milliseconds and inference time is 1 ms per image.