Various chemical compounds in green coffee beans are precursors of coffee beverage sensory attributes. The hypothesis was that those chemical compounds would vary with microclimate over the vertical plant profile of coffee plants. The plants of the cultivar IAPAR 59 were grown in two high plant densities (6000 and 10,000 plants ha−1) under rectangular and square planting patterns. Coffee beans were collected from three canopy strata. Chemical compounds and chlorogenic acid isomer (CGA) contents were determined by near infrared spectroscopy and ultra-performance liquid chromatography, respectively. The free-choice profile technique was employed to estimate the sensory attributes of coffee beverage. Brightness, transparency appearance, typical coffee color and aroma, tastes as sweet, acid, astringent and bitter, and full-bodied texture were attributes detected by panelists. Plants cultivated under lower plant density had lower leaf area index indicating lower self-shading than under higher plant density. Coffee beans originated from the inferior stratum of higher density had the lowest concentrations of 5-caffeoylquinic acid (5-CQA), while the inverse situation occurred in their upper strata. Strata of lower planting density were associated to high levels of all CGA isomers. The coffees cultivated under higher density showed high lipids and CGA isomers contents. Under lower density, beans had low concentration of sucrose, proteins, and caffeine and high of CGA isomer contents. The beverage sensory attributes depended on the concentration of proteins, lipids, and sucrose in combination to CQA isomers in beans, varying over the vertical profile and planting designs of coffee plants.