Applications running in a managed environment tend to require more system resources than similar applications that access machine resources more directly.

All "managed" languages are easier to reverse-engineer than native code. There is concern over possible loss of trade secrets and the bypassing of license control mechanisms. Microsoft's Visual Studio 2005 (and newer) includes a tool to obfuscate code, and many other techniques can help to prevent this.

Newer versions of the framework (3.5 and up) are not pre-installed in versions of Windows below Windows 7. For this reason, applications must lead users without the framework through a procedure to install it. Some developers have expressed concerns about the large size of .NET framework runtime installers for end-users. The size is around 54 MB for .NET 3.0, 197 MB for .NET 3.5, and 250 MB for .NET 3.5 SP1 (while using web installer the typical download for Windows XP is around 50 MB, for Windows Vista - 20 MB). The size issue is partially solved with .NET 4 installer (x86 + x64) being 54 MB.

The first service pack for version 3.5 mitigates this concern by offering a lighter-weight client-only subset of the full .NET Framework. Two significant limitations should be noted, though.Firstly, the client-only subset is only an option on an existing Windows XP SP2 system that currently has no other version of the .NET framework installed. In all other scenarios, the client-only installer will install the full version of the .NET Framework 3.5 SP1. Secondly, the client-only framework does not have a 64-bit option. However, the 4 release of the .NET Framework Client Profile will be available on all operating systems and all architectures (excluding ia64) supported by the full .NET Framework.

The .NET framework currently does not provide support for calling Streaming SIMD Extensions (SSE) via managed code. However, Mono has provided support for SIMD Extensions as of version 2.2 within the Mono.Simd namespace; Mono's lead developer Miguel de Icaza has expressed hope that this SIMD support will be adopted by the CLR ECMA standard.Streaming SIMD Extensions have been available in CPUs since the introduction of the Pentium III. However, adding CPU specific implementations would reduce the portability of .Net, one of its design goals.