The retailer said the loss amounted to 16 cents per diluted share for the quarter ended Sept. 29 compared with a loss of $35.1 million or $1.14 per diluted share a year ago when the company took a $25.4-million charge to goodwill.
Revenue for the quarter amounted to $185.6 million, down from $197.2 million a year ago.
The drop came as same-store sales at the retailer's Indigo and Chapters superstores fell 6.5 per cent, while its small-format Coles and IndigoSpirit stores saw sales fall 2.2 per cent.
"We are focused on driving significant margin and productivity improvements and are pleased that our ongoing efforts are reflected in our results," chief executive Heather Reisman said in a statement.
"We will continue to broaden our assortment in our key growth categories to drive higher top line sales to offset the decline in physical books. We're also pleased to have the newest Kobo e-readers now in store as top gift picks for the upcoming holiday season."
Indigo is Canada's biggest bookstore operator and runs stores under the names Chapters, Indigo and Coles.
Shares in the company, which reported its results after the close of markets, closed up 10 cents Tuesday at $9.50 on the Toronto Stock Exchange.