The time and cost benefits of rapid, object-oriented development attracted major corporations to WebObjects in the early days of e-commerce, with clients including BBC News, Dell Computer, Disney, DreamWorks SKG, Fannie Mae, GE Capital, Merrill Lynch, and Motorola.

Many early adopters later switched to alternative technologies, including Apple which had been the last remaining large client for the software, relying on it to power parts of its online Apple Store and the iTunes Store – which was WebObjects' highest-profile implementation at the time.

WebObjects was part of Apple's strategy of using software to drive hardware sales, and in 2000 the price was lowered from $50,000 (for the full deployment license) to $699.

From May 2001, WebObjects was included with Mac OS X Server, and no longer required a license key for development or deployment.

WebObjects transitioned from a stand-alone product to be a part of Mac OS X with the release of version 5.3 in June 2005.

In 2006, Apple announced the deprecation of Mac OS X's Cocoa-Java bridge with the release of Xcode 2.4 at the August 2006 Worldwide Developers Conference, and with it all dependent features, including the entire suite of WebObjects developer applications: EOModeler, EOModeler Plugin, WebObjects Builder, WebServices Assistant, RuleEditor and WOALauncher.

The main open-source alternative – the Eclipse IDE with the WOLips suite of plugins – had matured to such an extent that its capabilities had, in many areas, surpassed those of Apple's own tools, which had not seen significant updates for a number of years.

For example, Project Wonder has updated development tools and provides a REST framework that was not part of the original WebObjects package.

Though once included in the default installation of Mac OS X Server, WebObjects was no longer installed by default starting with Mac OS X Snow Leopard Server and shortly after, Apple ceased promoting or selling WebObjects.

As of 2016, WebObjects is actively supported by its developer community, the "WOCommunity Association", by extending the core frameworks and providing fixes with Project Wonder.

The two frameworks available are SOPE,[23] which has been used as the basis of the OpenGroupware.org groupware server for about eight years, and GNUstepWeb, which is part of the GNUstep project.