Seattle First Presbyterian's decision to disaffiliate from its denomination sets the stage for a battle over valuable downtown property.

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A real-estate battle is shaping up between a historic downtown Presbyterian church and the regional body that until now has governed it. At stake: nearly $29 million in assets.

On Sunday, Seattle First Presbyterian church members voted to split from its liberal-leaning denomination, the Presbyterian Church (U.S.A.). In doing so, the 125-member congregation formed a corporation that now claims full control of its assets, according to documents distributed Tuesday night at a meeting of the Seattle Presbytery, the denomination’s regional authority.

The church, founded in 1869, sits on a $20 million piece of property that stretches from Seventh to Eighth avenues along Spring Street. Also in contention, according to recently resigned church elder Neal Lampi and other sources, is $8.5 million reaped from selling a parking lot the church owned next to nearby Town Hall.

The Seattle Presbytery maintains churches cannot unilaterally disaffiliate but must go through a months-long separation process that includes negotiation over assets. What’s more, it holds that church property is held in trust for the denomination.

On Tuesday, the presbytery voted to establish an “administrative commission” to investigate the actions by Seattle First Presbyterian, Scott Lumsden, head of the regional body confirmed. He declined further comment.

According to the documents distributed, the commission will delve not only into the church’s unorthodox move to separate but allegations of irregular proceedings, secrecy, intimidation of dissenters and its consideration of transferring funds to its spinoff corporation or its attorneys.

According to a presbytery summary distributed Tuesday, the church has already acknowledged putting $420,000 into a trust account of the Seattle law firm Lane Powell.

“These allegations, admissions, and events suggest that the [church’s leadership] is affected with disorder … and call into question its ability and willingness to exercise its authority and to wisely manage its affairs,” the summary goes on.

The presbytery authorized the commission to assume control of the church and “dissolve pastoral relationships” if necessary.

It would not be the first time.

Lumsden, in a letter last week to the Seattle First Presbyterian congregation, pointed to a 1971 Washington state Supreme Court case involving a Laurelhurst Presbyterian church that attempted to separate from the presbytery over a doctrinal dispute. The church claimed its property. The presbytery objected and staged a take over — one ultimately sanctioned by the court.

A Nov. 2 letter to the presbytery’s lawyers from Lane Powell, on behalf of Seattle First Presbyterian, did not mention this precedent, instead warning of the dangers of a legal fight. “As you are no doubt aware, disaffiliation issues have spilled into courts all over the country and have generated legal expense for all concerned parties.”

Several local Presbyterian churches have recently left the Presbyterian Church (U.S.A.) on good terms, according to Lumsden. Yet around the country, real estate fights have broken out among Presbyterian and Episcopal denominations as churches defected over liberal policies, particularly around gays and lesbians.

In an interview last week, Seattle First Presbyterian co-pastors Jeff and Ellen Schulz denied that their desire to leave the denomination stemmed from its recent decisions to ordain gay and lesbian clergy and accept same-sex marriage.

Lampi said otherwise. He noted Seattle First Presbyterian’s leadership began portraying the denomination as un-Christlike after the 2011 ordination decision, and voted not to ordain gays and lesbians at their church.

The church, with a congregation massively diminished from its heyday of 8,000 members, subsequently began talking about a merger with a new church started by former Mars Hill pastor Tim Gaydos. The presbytery objected to the merger, igniting another source of conflict, according to a letter from Seattle First Presbyterian’s leadership to the congregation before the disaffiliation vote.

“In light of the value of our property and our plans to develop it, we expect that control over our assets will be an ongoing source of tension in our relationship with the presbytery,” the letter continued.

“This conflict has consumed me,” said Lampi, who consequently resigned as elder and director of the church’s homeless shelter.

In an indication of the tensions at play, the church had security guards at its Sunday vote. Rajat Parsad, baptized at the church in 2013 but a lapsed attendee, said he went to express his dissent over the proposed split, but was forcibly removed from the building by the guards when his membership was challenged. After loudly protesting, Jeff Schulz, the pastor, came out of the church and agreed to let him back in, according to Parsad and his videos of the skirmish.

“A disruptive situation was resolved,” wrote Jeff Schulz in an email.

As for the larger conflict with the presbytery, he said he expected to be in communication with the new commission “to address our mutual concerns.”