Confirm the leak path. If it's safe and you have a helper, a controlled hose test works: one person inside watches; the other wets small roof sections starting low and working upward. Don't blast the roof like a pressure washer—steady water is better for pinpointing the exact entry point.
Open the area gently. For shingle work, lift the shingle above the damaged one to expose nails. Remove nails, slide out the damaged shingle, and scrape away old brittle cement only where it prevents a flat fit. If the decking under the shingle is soft, punky, or delaminating, stop and reassess—patching over rotten wood is a short-lived victory.
Make the repair that matches the failure. Missing, cracked, or torn shingles: replace the shingle. Slide the new shingle into place, align exposure, nail in the manufacturer nail zone, and seal the lifted tabs. Keep nails where they'll be covered by the shingle above so water never hits fastener heads directly.
Nail pops: pull the popped nail, press the shingle flat, and renail nearby (not in the same elongated hole). Seal the old hole and the new fastener head. Nail pops often happen where decking expands and contracts, so the new fastener should go into solid wood slightly offset from the old location.
Pipe boot leaks: if the rubber is cracked or the boot is loose, replace the boot. This typically involves loosening the shingles around it, removing old nails, sliding the old boot out, sliding the new one in under the upper shingles, and then re-nailing and resealing. A boot that's merely caulked to death is usually telling you it's past its best days.
Sidewall and step flashing leaks: this is where careful home roof repairs shine. Step flashing should be layered with each course of shingles so water is always directed onto the shingle below, not behind it. If step flashing is missing, rusted, or installed as one long piece where steps should be, you'll often see repeated stains inside. Rework the detail with individual step pieces, weave them with shingles, and use appropriate sealing at overlaps—without creating a dam.
Chimney flashing issues: chimneys are notorious because they mix masonry movement, thermal cycling, and multiple flashing pieces. If metal is visibly separated, bent, or corroded, you may need a more involved rebuild than a simple seal. If the chimney is tall, steep-roofed, or the masonry is failing, that's not a learn-on-the-fly moment—call a professional.
Prove it and clean up like you mean it. After the repair, do another controlled hose test or wait for the next rain and inspect. In the attic, check that damp insulation is drying and that no new shiny nail tips appear. Outside, run a magnet sweeper around your work area. A roof repair home project that ends with nails in the driveway is the kind of project you only do once.