Jayson Joseph Michaels, from the town of Bindoon north of Perth, appeared in Perth Magistrates Court on Friday, facing five charges, including acting in preparation for a terrorist act.
WA's Premier Roger Cook said the 20-year-old was allegedly plotting to attack public buildings, including the WA parliament and mosques.
"Police allege the man was planning a mass casualty event on a range of public buildings across Perth, including the WA police headquarters, WA Parliament House and Muslim faith places of worship," he told reporters.
"It will be alleged this person was motivated by a white supremacist ideology."
A joint counter-terrorism team began investigating Michaels in January after it received intelligence about encrypted communications concerning white supremacist ideology, anti-Muslim ideology, and anti-Semitism.
WA Police Commissioner Col Blanch said investigators also found "abhorrent" conversations about minorities and other races in the messages.
Officers swooped on Michael's home on Thursday after identifying him as the alleged source.
"We observed and have now seized firearms, imitation firearms, a ballistic vest, gas masks, and lock-picking equipment," Mr Blanch said.
"Most concerning, there was a notebook that outlined preparations for a terrorist attack at significant locations."
It will be alleged that Michaels was acting alone and had written a "concerningly detailed" manifesto outlining plans for an ideologically motivated "extremely serious terrorist attack" involving firearms and explosives.
Officers seized seven rifles from Michael's property, and police had no intelligence about him before the investigation started.
"The fact that someone can be online and be radicalised so easily, and have no record about their history ... that's what should concern us," Mr Blanch said.
Authorities continued to investigate the encrypted communications platform, which contained conversations with people from outside Australia sharing white supremacist ideology.
Michaels has also been charged with using a carriage service to menace or harass, possessing a prohibited weapon and two firearms offences.
He was remanded in custody to reappear in the same court on March 23.