The stock briefly lost 3.8 percent to $45.76 a share before recovering much of its losses and closing 0.48 percent lower.
Square is a "collection of yawn businesses," Citron said in a tweet Monday afternoon. "WallSt. drunk on Bitcoin nonsense. SQ-Cash to BTC trading has been insignificant. Even w/ hyper growth still 40% too rich."
Citron also set a short-term price target of $30 on the stock, or 36.9 percent below Friday's close.
Shares are little changed since Square, run by Twitter co-founder Jack Dorsey, launched bitcoin trading in late January for most users of its Cash mobile payments app.
Bitcoin surged in popularity over the last year, hitting a record high above $19,000 in December. It traded near $9,300 Monday, still up 570 percent over the last 12 months.
"I think the bitcoin impact will be material long term," Nomura Instinet research analyst Dan Dolev said in a phone interview Monday.
He raised his price target on Square to $65 on April 18, based on the view that launching bitcoin trading could add up to 10 percent to adjusted earnings before interest, taxes, depreciation and amortization.
Square is up 34 percent for the year so far. The company did not immediately respond to a CNBC request for comment.