Francis was only on the field for eight minutes as he appeared for Saints for the first time since the start of November.
It was just his third game of an injury-hit campaign and he was visibly upset as he headed down the tunnel to be replaced by Fraser Dingwall.
Boyd was asked about Francis's injury after Saints' 30-6 defeat to Saracens at cinch Stadium at Franklin's Gardens.
And the Saints boss said: "He's done something to his foot.
"It's not going to be a massive setback - it's going to be weeks not months by the look of it.
"But I felt deeply sorry for him because he's worked so hard to get back.
"But it looks like he's done a mischief to his foot again."