Each episode of Top Chef, save for the finale, has had two challenges.

In the Quickfire Challenge, each chef is asked to cook a dish with certain requirements (for example, using specific ingredients or to inspire a certain taste) or participate in a culinary-related challenge (for example, a mise en place relay or a taste test). They are usually given an hour or less to complete these tasks. A guest judge selects one or more chefs as the best in the challenge. In most cases, the winning chef(s) are granted immunity from the following Elimination Challenge, though they may also gain an additional reward (such as being team captains for a team challenge).

In the Elimination Challenge, the chefs have to prepare one or more dishes to meet the challenge requirements. Many of these are individual challenges and may require several courses, although some instances require teams to complete the challenge. Teams may be selected by the remaining contestants among themselves, but more often are selected by the random process of "drawing knives" from a butcher's block, with the team identification revealed on the blade of the knife. The chefs may have from a few hours to a few days to complete this challenge. Ingredients for Elimination Challenges are generally limited to what is present in the "Top Chef" pantry and what the chefs purchase at a food store, with a possibly limited budget. However, certain challenges may provide specific ingredients or limit the type or number of ingredients that can be used, while others require non-traditional methods of obtaining ingredients (such as asking people door-to-door). After shopping, the contestants will cook for four judges, usually including at least one guest judge. In most cases, the contestants cook for the four judges and a group of guests or customers (for example, the cowboys in Colorado). The judges and the guests sample the food and rate the individuals or teams.

After the Elimination Challenge ends, the chefs are taken to Judges' Table, where the four judges consider the guests' comments and deliberate on the best and worst dishes. The top individuals or teams are called in, and may be asked questions of their meals before they are notified of their placement. One individual is named the winner of the challenge and may be awarded an additional prize by the guest judge. Then, the bottom individuals or teams are brought to the judges, and similar discussion of their courses is played out. From this group, one chef or team is determined to be the worst, and then the host asks one chef to "pack [their] knives and go." This is usually followed by a knife packing sequence for the eliminated chef, and a clip of his or her exit video, to close out the episode. According to the credits, some elimination decisions (eg. Cliff Crooks's disqualification in Season 2) are made in consultation with the show's producers.

The show continues in this format for 10-13 episodes, until the Finale.

Midway through each season, the contestants participate in a "Restaurant Wars" (or similarly named) Elimination Challenge. They are split into two teams, created by the winner of the previous Quickfire Challenge, or by "drawing knives". In these teams, the chefs must transform an empty space into a restaurant within a set time limit and budget, selecting and creating the name, theme, decor, and menu. According to Dale Levitski, a Season Three finalist, this is one of the contestants' most anticipated challenges. Season Four had not only "Restaurant Wars", but also "Wedding Wars".

In the final challenge, the two (or three) remaining chefs prepare a multiple course dinner with the help of other chefs. These other chefs could be previously eliminated chefs or celebrity chefs (for example, Rocco DiSpirito). The winning chef is selected based on several factors including food quality, their ability to lead their selected chefs, and general performance during the show. There is no Quickfire Challenge in this episode.

There have been 48 guest judges so far on all 4 seasons. Of these, 16 have won the Food and Wine Best New Chef award, including Head Judge Tom Colicchio. Of these 48 guests, 9 have appeared multiple times. Anthony Bourdain leads with 5 appearances, Rocco DiSpirito* and Eric Ripert with 3 (Ripert appeared a fourth time on the Top Chef Holiday Special, see below), and the rest tie with two: Wylie Dufresne*, Hubert Keller*, Daniel Boulud*, Michelle Bernstein, Ming Tsai and Mike Yakura. Of these 9, 4 were winners of Food and Wine Best New Chef. During season 5, the Foo Fighters guest judged a Thanksgiving dinner.

• Ted Allen is from Queer Eye for the Straight Guy and Uncorked: Wine Made Simple on PBS.
• Gail Simmons is from Food & Wine Magazine.
• Padma Lakshmi is an actress, model, and cookbook author.
• Tom Colicchio is a chef & owner of Gramercy Tavern & Craft restaurants.

Season 1: Harold Dieterle, Runner Up: Tiffani Faison

Season 2: Ilan Hall, Runner Up: Marcel Vigneron

Season 3: Hung Huynh, Runners Up: Dale Levitski and Casey Thompson

Season 4: Stephanie Izzard, Runners Up: Richard and Lisa

Season 5: Hosea Rosenberg