There are three botanical varieties of cacao. Criollo trees produce mild beans with delicate flavors; Forastero trees provide full-flavored beans and comprise 95% of the world's production; Trinitario trees are hybrids with intermediate qualities. Cacao beans are composed of white cells that contain cocoa fat and purple cells that contain polyphenols, anthocyanins, theobromine, and caffeine (which act as defensive molecules against animals).

Straight out of the cacao pod, the bean is bitter, astringent, and without flavor. It is in the processing that cacao bean's flavors develop due to over 500 compounds. The first step in developing chocolate flavor is fermentation and drying, which takes place on the plantation, with tremendous variation in quality control. After harvesting, the cacao pods are broken open to expose the sugary pulp and beans. At ambient temperature in less than 8 days, yeast, anaerobic bacteria, then aerobic bacteria converts the sugar in pulp to alcohol and then into vinegar (acetic acid) similar to how grapes are fermented into wine and vinegar. The acid first etches small pores then penetrates through the bean husk, thereby disrupting the integrity of interior white and purple cells and allowing their contents to interact  to generate aromatic precursor molecules. Beans also absorb the essence of sugars and fruity, flowery notes from the surrounding fermented pulp. The beans are subsequently dried by spreading them out in the sun to remove moisture, slow microbial growth, and oxidize polyphenols (browning) that reduce bitterness. After this stage, they are shipped to manufacturers.

The second major step in developing chocolate flavor is through gently roasting the beans at 250-320° F (120-160° C). After roasting, the beans are cracked open and the thin shell separated from the inner kernels of the fruit meat ("nibs"). When passed between rollers, the nibs are converted to "cocoa liquor", a thick dark fluid composed of cell fragments and cocoa butter. Pressed through a filter, the particles and butter are further separated. Grinding of the solids then reduces the particulate size to a smooth consistency. Unsweetened or baking chocolate is this chocolate liquor. At this point, however, the cacao solids are still not edible until cocoa butter and sugar is added to create dark chocolate, or sugar and milk solids added to create milk chocolate. The reintroduction of cocoa butter lubricates the sugar particles and avoids a pasty consistency. A conche machine smears the mixture using rollers for up to 36 hours, coating the particulates evenly with cocoa, while aerating and gently heating (by friction) the volatile, undesirable aromatic compounds until they evaporate. The heat also generates caramel, roasted, and malt flavor notes. Lecithin also may be added to coat sugar particles and lessen the amount of cocoa butter needed. 

Finally, the liquid chocolate is cooled, then carefully rewarmed before cooling down into chocolate bars. This phase transition from liquid to solid must be accomplished by a processing called "tempering" to generate stable crystals of cocoa fat with a desirable appearance and snap.  

The three varieties of solid eating chocolate are dark, milk, and white. Dark chocolate contains only cocoa solids, cocoa butter, and sugar (on labels, “70% chocolate” means 30% sugar). Semisweet or bittersweet chocolate is at least 35% chocolate liquor by weight. Milk chocolate, in contrast, includes milk solids and usually, a larger proportion of sugar. In most of Europe, dried whole milk powder is used to make milk chocolate (imparting a fresh-milk flavor). In England, liquid milk is mixed with sugar, concentrated, added to chocolate liquor, and dried (imparting caramelized-milk flavor). In the U.S., milk fat is first broken down by enzymes before adding (imparting a slightly cheesy aroma). White chocolate is distinct in that it is chocolate-less chocolate, only containing cocoa butter, milk solids, and sugar, but no cocoa solids at all. Outside of Europe, white chocolate is often made with vegetable fat rather than cocoa butter and less flavorful and silky than the real thing.

A bar of chocolate should have a sharp snap when broken, and produce even-textured fissures with no splinters or crumbs, and should melt smoothly on the tongue with a rich, nutty slightly acidic flavor.

Chocolate has a unique chemical composition, which account for its unique texture. Because chocolate’s fat base (cocoa butter) is nearly all saturated (i.e. containing single bonds), its molecules are able to stack tightly and regularly, forming non-greasy slabs of dry, brittle chocolate. This tight, stable packing can only occur when chocolate has been formed through careful, controlled warming and cooling (tempering), so chocolate that has melted and only casually been reformed (think chocolate bars left in hot cars then thrown in the refrigerator to resolidify) is no longer the same.

Nearly all chocolate that is sold has been tempered. This requires heating the chocolate to melt all fat crystals, then cooling slightly to generate starter crystals, then melting carefully to melt only the unstable versions but maintain stable crystals - a situation that occur at the narrow window of 88-90°F (31-32° C). Once tempered chocolate is overheated and melts completely so all of its fat crystals disappear, it will not properly reform without tempering again. In contrast, chocolate may be melted while maintaining it in temper by using a double boiler (bowl set over a pan of hot water), finely chopped chocolate, and heating to only 90-95° F (32-34° C).

Chocolate is best stored at room temperature, specifically 60-65° F (15-18° C) without fluctuations that would cause melting and recrystallization. Stored chocolate bars may develop a white powdery coating ("fat bloom") that consists of cocoa butter that has melted out of unstable crystals, migrated to the surface, and reformed crystals.

When baking or cooking with chocolate, it is important to use the precise type of chocolate called for in the recipe. The distinct amounts of cocoa butter, cocoa solids, sugar, and milk in different chocolates can have a significant effect on the final outcome. For example, if chocolate is too sweet, it will become overly fluid-like when its excess sugar combines with water in the recipe. Chocolate with more cocoa solids (a higher percentage chocolate on the label) can soak up moisture and make a mixture too dry. Therefore, you cannot "make-do" with 70% dark, bittersweet chocolate in a recipe that calls for “milk chocolate”.

Chocolate should be stored in a cool, dry place and wrapped tightly to protect against moisture and odor absorption. Perhaps due to plentiful polyphenols that serve as antioxidants, chocolate has a shelf life of up to two years; in contrast white chocolate, which is devoid of polyphenols from absent cocoa solids, is sensitive to light, and lasts only a few weeks after which it becomes rancid.

Cacao, contains a high concentration of phenolic molecules that have anti-angiogenic activity. Unfermented, sun-dried cocoa beans have a total polyphenol content of 7g/100g. Fermentation and roasting, which renders the familiar chocolate flavor, retains polyphenols to a level of 2 g/100g). Cocoa powder, the defatted part of the cacao bean, has one of the highest concentration of polyphenols of any food, over 8% by total weight. Proanthocyanidins account for 60% of the total polyphenol content in cacao. Proanthocyanidins are polymers of flavonoid molecules similar to that in green tea (epicatechin), and are found in other foods including cranberries, cinnamon, apples, grapes, black currant, chokeberry and persimmon.  Several in vitro studies have demonstrated anti-angiogenic effects of these molecules. Procyanidins in cacao inhibit the growth of human endothelial cells that comprise blood vessels. In laboratory studies, cocoa polyphenols inhibited expression of the pro-angiogenesis growth factor VEGF by more than two-fold.

Several studies have examined the effects of chocolate and cocoa powder in people. Participants consuming 40g/day of cocoa powder in milk exhibited significantly lower serum concentrations of soluble cell adhesion molecules derived from blood vessel cells that assist the binding of tumor cells to blood vessels. The Kuna Indians living on an island off Panama drink more than 5 cups of cacao each day and compared to mainlanders, have a six-fold higher urinary excretion of cacao procyanidin metabolites, and have a lower incidence of cancer. In the Leisure World Cohort Study, subjects who reported occasional chocolate intake had a statistically significant lower mortality by 6%.