House Bill 2149 passed just before midnight on a 67-29 vote. It now heads to the Senate, which is considering similar measures addressing how to reconcile the two marijuana systems.
Changes under the bill sponsored by Democratic Rep. Eileen Cody include reducing the amount of marijuana and number of plants patients can possess, doing away with collective gardens and establishing a patient registry.
Cody said that lawmakers are trying to align the systems, "but continue to make sure our legitimate medical marijuana patients have access."
"I think that we can satisfy some of the patients," she said after the vote. "I don't think that all of the medical marijuana community will be happy."
The state has allowed medical use of marijuana since 1998. The passage of Initiative 502 in 2012 allowed the sale of the drug to adults for recreational use at licensed stores, which are expected to open by this summer.
Lawmakers have worried that the largely unregulated medical system would undercut the taxed, recreational industry, and U.S. Justice Department officials have warned that the state's medical pot status quo is untenable.
Medical marijuana patients have flocked to public hearings on the issue in both the Senate and House in recent weeks, decrying the potential changes.
Rep. Cary Condotta, R-East Wenatchee, said HB 2149 was premature because the recreational system is not yet up and running, adding that the impact on medical marijuana patients should be looked at more closely.
"Right now, you're taking everything away from them - you can't give it back," he said during the floor debate. "I'm a little concerned we're moving a little too quickly without a program to integrate."
In December, the state's Liquor Control Board gave its final recommendations to the Legislature about how it believes the medical system can be brought under the umbrella of I-502.
Cody's bill incorporates many of those suggestions, including cutting how much pot patients can have from 24 ounces to 3 ounces - which is still more than the 1 ounce adults are allowed under the recreational law. However, Cody's measure allows a health care professional to authorize more if deemed necessary. Her measure also limits the number of plants patients can grow to six. Under current regulations, they can grow 15.