Empire Earth II has several new gameplay features from the original gameplay of Empire Earth, such as the Picture-in-Picture window, a small window within the game interface which allows the player to control activities such as unit and building construction. The Citizen Manager can be configured to tell a citizen what to do if they have no set task, and the Diplomacy System allows the player to make tributes and manage alliances and wars with other players. The War Planner is another new addition, which is a map of the game that the player can display and use to coordinate attacks with allies. The crown system grants strategic bonuses to players who are first to master an epoch's military, economic, or imperial paths at the cost of losing a faster age progression. Weather, another new feature, changes over time on the map and affects the look of the map and performance of units and, in the case of airplanes in thunderstorms, hit points.

Besides campaigns and special scenarios, there is also a skirmish mode where the player can play against a computer player. The player can also play against other human players, however, the common EULA clause that each player needs his own copy of the game is actually enforced, even for LAN games. Unlike campaigns or scenarios, the winning conditions never change. There are eight different game modes in skirmish mode, which can also be played in Multiplayer. The multiplayer servers were taken offline on 1 November 2008, after which players can only play through local area network. The Multiplayer GameSpy servers were taken offline on 10 October 2012. 

There are 15 epochs in the game, each representing a part of history. As the player advances through the epochs, new and improved units and structures become available. Some of the epochs in EE2 are identical to their counterparts in the original Empire Earth—one exception is that EE2 does not allow players to expand their empires into space. The epochs are the Stone Age, Copper Age, Bronze Age, Iron Age, Dark Ages, Middle Ages, Renaissance, Imperial Age, Enlightenment Age, Industrial Age, Modern Age, Atomic Age, Digital Age, Genetic Age and Synthetic Age.

Before buildings and units can be made or created, resources must be gathered. There are two kinds of resources: main resources and special resources. The main resources are available in all epochs and they are food, wood, gold, and stone. To collect resources, a citizen (or a band of citizens) is selected, and are directed to a resource. The citizens thus begin harvesting it.

The special resources are available in only some epochs. These special resources are tin—available until epoch 6, iron—first available in epoch 4 and is no longer used after epoch 9, saltpeter—first available in epoch 7 and is used until epoch 12, oil—first available in epoch 10, and uranium—first available epoch 13.

EE2 has technologies to improve each player's civilization. Technologies are divided into three groups. The first is Military, which provides benefits mostly to military units. The next is Economic technologies, which increases resource gathering rate, decreases cost and building time for units and buildings and decreases tribute tax amount. The final group is Imperial, which provides benefits mostly to special units and increases the health of units and buildings.

There are four technologies of each group for each epoch. Technologies can be researched by spending tech points. To get tech points, an appropriate number of citizens must be garrisoned in a university and/or an appropriate number of priests must be garrisoned in a temple. Technologies are researched through the main interface (no longer through a building) by clicking the Technology Tree button. When the correct amount of tech points are available, the tech tree button will light up and a new technology to research can be chosen. However, when research is no longer used (at the highest epoch specified before starting a game), the garrisoned units will become idle.

In EE2, each civilization belongs to a particular world region, each having its own regional powers. These can be activated on the game interface by clicking on a crown in the top right corner. All of the regional powers are timed; once the time is up to use it, it takes a long time for the regional powers to be recharged to use again. Each regional power can only be used in a respective group of epochs. For example, the regional power of Overtime can only be used by a player using a Far Eastern civilization in epochs 11-15.

Like many games before it in the same genre, EE2 has civilizations for players to lead to greatness. Each civilization has a unique power, giving it an advantage in a particular field. Each civilization also has a unique unit, which is a more powerful version of a given unit type. The Greek Hoplite, for instance, is a more effective heavy infantry than other tribes counterparts. The western civilizations are the Americans, British, Germans, Greeks, and the Romans. The Middle Eastern civilizations are the Babylonians, Egyptians, and the Turks. The Far Eastern civilizations are China, Japan, and Korea. Finally, the Meso-American civilizations are the Aztecs, Incas, and the Mayans.