Coffee is one of the most consumed products worldwide. Among the varieties of this product, specialty coffee is a type of coffee that has been growing in the world market. This paper aims to assess the effects that the conditions derived from coffee roasting at different altitude levels have on the quality of the product. It was discovered that processing coffee at a higher altitude level yielded a smaller increase in bitterness. This led to a better Specialty Coffee Association (SCA) score in cupping and, consequently, to better preservation of the coffee quality. The storage time affected the aroma by associating roaster aromas with older coffees. Although the assessed origins had the same NIR spectra, differences in peak intensity lead to variations in the flavor and aroma of the coffee. Furthermore, although green beans prolong quality allowing a SCA score of 84.73 ± 2.81 after 4 months of storage, roasted coffee at higher altitudes could also maintain the quality between production and consumption (SCA score of 80.22 ± 0.91 after 2 months). Finally, this research found that the instrumental equipment helped to find minor changes in the sensorial profile, and with these changes correlated with the sensorial panel, the best conditions to preserve coffee quality were found.