McManus, who had reached his fifty earlier from 97 balls, marshalled the lower order superbly during the first half of the day and found a willing assistant in Calvin Harrison.
The loan signing from Nottinghamshire gave steady support in an 81-run partnership inside 30 overs for the eighth wicket that included reverse sweeping Tom Hartley for four to reach his half-century from 87 balls.
It proved to be a frustrating passage of play for Lancashire who bowled spinners Hartley and Luke Wells in tandem for the final 33 overs of the innings in an attempt to dry up the run scoring and exert some pressure.
The innings ended abruptly with the final three wickets falling for 12 runs, starting when McManus became the second Northamptonshire batter to fall agonisingly short of a hundred in two days.
Having seen James Sales perish for 92 on Friday, McManus departed in similar fashion on 95, top-edging a front-foot slog off a Wells delivery pushed wider that went high to Bohannon at mid-off.
Hartley (3-91) then wrapped things up bowling both Liam Guthrie for a duck and Harrison for 56 via inside edges.
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