Leaf Soil-Plant Analysis Development (SPAD) prediction is a crucial measure of plant health and is essential for optimizing indoor plant management. The deep learning methods offer advanced tools for precise evaluations but their adaptation to the heterogeneous indoor plant ecosystem presents distinct challenges. This study assesses how accurately deep neural network (DNN) predicts SPAD values in leaves on indoor plants when compared to well-established machine learning techniques, including Random Forest (RF) and Extreme Gradient Boosting (XGB). The covariates for prediction were based on low-cost multispectral and soil electro-conductivity (EC) sensors, enabling a non-destructive sensing approach. The study also strongly emphasized multicollinearity analysis quantified by the Variance Inflation Factor (VIF) and two independent indices, as well as its effect on prediction accuracy using deep and machine learning methods. DNN resulted in higher accuracy to RF and XGB, also performing better using filtered data after multicollinearity analysis based on the coefficient of determination (R2), root mean square error (RMSE) and mean absolute error (MAE) (R2 = 0.589, RMSE = 11.68, MAE = 9.52) in comparison to using all input covariates (R2 = 0.476, RMSE = 12.90, MAE = 10.94). Overall, DNN was proven as a more accurate prediction method than the conventional machine learning approach for the prediction of leaf SPAD values in indoor plants, despite using heterogenous plant types and input covariates.