Clough's 11th minute lob gave Wanderers a perfect start and the visitors were then indebted to Lee Burge for keeping them in the contest.
The City keeper saved from Gary Madine, Josh Vela and Clough on a night when former Bolton player and coach Gary Speed was honoured with a minute's applause by fans.
But if Burge excelled in the opening period, opposite number Ben Alnwick came to the Trotters' rescue in the second.
Having already denied Kyel Reid before the break, Alnwick saved superbly from Lewis Page plus substitutes Jodi Jones and Ruben Lameiras.
Bolton's best moment of the second half was Clough's 25-yard free-kick, which was tipped on to the post and away to safety by the outstanding Burge.
Coventry poured forward in search of a late equaliser to try to avoid a third straight league defeat, but instead, Phil Parkinson's side held on for their first home win over the Sky Blues in eight attempts since 1965.
Report supplied by Press Association.
Match ends, Bolton Wanderers 1, Coventry City 0.
Second Half ends, Bolton Wanderers 1, Coventry City 0.
Attempt missed. Gael Bigirimana (Coventry City) right footed shot from outside the box is close, but misses to the left.
Foul by James Henry (Bolton Wanderers).
Ben Stevenson (Coventry City) wins a free kick in the attacking half.
Josh Vela (Bolton Wanderers) wins a free kick in the defensive half.
Foul by Jordan Turnbull (Coventry City).
Substitution, Bolton Wanderers. Jamie Proctor replaces Gary Madine.
Corner,  Coventry City. Conceded by Lawrie Wilson.
Corner,  Coventry City. Conceded by Lawrie Wilson.
Attempt blocked. Jack McBean (Coventry City) right footed shot from the centre of the box is blocked.
Attempt missed. Jamie Sterry (Coventry City) right footed shot from outside the box is high and wide to the right.
Foul by Gary Madine (Bolton Wanderers).
Jordan Willis (Coventry City) wins a free kick in the attacking half.
Attempt missed. Ruben Lameiras (Coventry City) left footed shot from the right side of the box is close, but misses to the left.
Substitution, Coventry City. Jack McBean replaces Kyel Reid.
Corner,  Coventry City. Conceded by Jay Spearing.
Attempt missed. James Henry (Bolton Wanderers) left footed shot from the centre of the box is just a bit too high.
Attempt missed. Kyel Reid (Coventry City) left footed shot from outside the box is too high.
Corner,  Coventry City. Conceded by Andrew Taylor.
Corner,  Coventry City. Conceded by Ben Alnwick.
Attempt saved. Ben Stevenson (Coventry City) right footed shot from outside the box is saved in the bottom left corner.
Lawrie Wilson (Bolton Wanderers) wins a free kick in the defensive half.
Foul by Kyel Reid (Coventry City).
Attempt blocked. Jordan Turnbull (Coventry City) header from the centre of the box is blocked.
Corner,  Coventry City. Conceded by Josh Vela.
Attempt blocked. Ruben Lameiras (Coventry City) right footed shot from outside the box is blocked.
Foul by Jay Spearing (Bolton Wanderers).
Kyel Reid (Coventry City) wins a free kick on the left wing.
Substitution, Bolton Wanderers. Chris Taylor replaces Sammy Ameobi.
Substitution, Bolton Wanderers. James Henry replaces Zach Clough.
Hand ball by Josh Vela (Bolton Wanderers).
Corner,  Coventry City. Conceded by Ben Alnwick.
Attempt saved. Ruben Lameiras (Coventry City) right footed shot from the centre of the box is saved in the top right corner.
Foul by Sammy Ameobi (Bolton Wanderers).
Kyel Reid (Coventry City) wins a free kick in the attacking half.
Corner,  Coventry City. Conceded by Ben Alnwick.
Attempt saved. Jodi Jones (Coventry City) left footed shot from outside the box is saved in the bottom left corner.
Marvin Sordell (Coventry City) is shown the yellow card for a bad foul.
Jay Spearing (Bolton Wanderers) wins a free kick in the attacking half.
Zach Clough netted his sixth goal in eight starts, but high-flying Bolton were made to work hard for their League One win over Coventry at the Macron Stadium.