Malnutrition is a multidomain problem affecting 54% of older adults in long-term care (LTC). Monitoring nutritional intake in LTC is laborious and subjective, limiting clinical inference capabilities. Recent advances in automatic image-based food estimation have not yet been evaluated in LTC settings. Here, we describe a fully automatic imaging system for quantifying food intake. We propose a novel deep convolutional encoder-decoder food network with depth-refinement (EDFN-D) using an RGB-D camera for quantifying a plate's remaining food volume relative to reference portions in whole and modified texture foods. We trained and validated the network on the pre-labelled UNIMIB2016 food dataset and tested on our two novel LTC-inspired plate datasets (689 plate images, 36 unique foods). EDFN-D performed comparably to depth-refined graph cut on IOU (0.879 vs. 0.887), with intake errors well below typical 50% (mean percent intake error: -4.2%). We identify how standard segmentation metrics are insufficient due to visual-volume discordance, and include volume disparity analysis to facilitate system trust. This system provides improved transparency, approximates human assessors with enhanced objectivity, accuracy, and precision while avoiding hefty semi-automatic method time requirements. This may help address short-comings currently limiting utility of automated early malnutrition detection in resource-constrained LTC and hospital settings.