An automated computer-controlled sampling system and related methods for collecting, processing, and analyzing agricultural samples for various chemical properties such as plant available nutrients. The sampling system allows multiple samples to be processed and analyzed for different analytes or chemical properties in a simultaneous concurrent or semi-concurrent manner. Advantageously, the system can process soil samples in the “as collected” condition without drying or grinding first to produce a sample slurry. The system includes a multi-layered microfluidic manifold chemical analysis substrate configured to provide a temperature-compensated concentration of analytes or other chemical properties associated with the sample. The system utilizes a programmable controller, temperature sensor, and absorbance measurement device for that purpose. The system can be used to analyze various type of agricultural-related samples including soil, vegetation, manure, milk or other.