Every Menards store shares a common structure. Each store is primarily divided by departments: building materials, hardware, electrical, millwork, wall coverings, plumbing and housewares, floor coverings, cabinets and appliances, and groceries. Other areas of the store include the front end (cashiers, office functions, carryouts, etcetera) and the receiving crew (responsible for the lumber yard, shipments between the store and the distributions centers, and other delivery and merchandise logistics). In a typical store there is a Store Manager, two Assistant Managers, a Department manager, and various Sales Floor team members , which is dependent upon the guest volume typical at that individual store. Some departments are combined dependent upon store volume and guest traffic or only have a single Assistant Manager.

Menards stores are divided into categories based on store size and product range. These categories range from P1 (Prototype size 1) to P5 (prototype size 5), Hardware Plus (smaller than a P1 with fewer building materials item selections) and non-prototype (usually stores that have moved into pre-existing locations or locations where large prototype stores will not fit, such as the 2-story stores).

Recently, the 240,000 sq ft (22,000 m) and larger Menards stores began selling groceries. By adding a second story mezzanine for less often accessed items, space can be made for groceries on the main floor.