A method, apparatus, and computer instructions are provided for inlining native functions into compiled Java code. A conversion engine is provided by the present invention for converting the intermediate representation of native functions to the just-in-time (JIT) compiler's intermediate representation. With the converted intermediate representation, an inliner recursively inlines the converted JIT compiler's intermediate representation into the native callsite to remove the need of invoking the native function and subsequent native calls made by the function. The inlining process continues until either a call to an opaque function is encountered or until a JIT compiler intermediate representation growth limits are reached. The inliner also replaces calls to most native functions that are non-inlineable or opaque with calls to synthesized native functions that provide access to native libraries containing implementations of the original non-inlineable calls.