diff --git a/scrape/scrape.go b/scrape/scrape.go
index dfa945852..383c262e0 100644
--- a/scrape/scrape.go
+++ b/scrape/scrape.go
@@ -1192,14 +1192,18 @@ mainLoop:
 		// Calling Round ensures the time used is the wall clock, as otherwise .Sub
 		// and .Add on time.Time behave differently (see time package docs).
 		scrapeTime := time.Now().Round(0)
-		if AlignScrapeTimestamps && sl.interval > 100*ScrapeTimestampTolerance {
+		if AlignScrapeTimestamps {
+			tolerance := ScrapeTimestampTolerance
+			if maxTolerance := sl.interval / 100; tolerance < maxTolerance {
+				tolerance = maxTolerance
+			}
 			// For some reason, a tick might have been skipped, in which case we
 			// would call alignedScrapeTime.Add(interval) multiple times.
 			for scrapeTime.Sub(alignedScrapeTime) >= sl.interval {
 				alignedScrapeTime = alignedScrapeTime.Add(sl.interval)
 			}
 			// Align the scrape time if we are in the tolerance boundaries.
-			if scrapeTime.Sub(alignedScrapeTime) <= ScrapeTimestampTolerance {
+			if scrapeTime.Sub(alignedScrapeTime) <= tolerance {
 				scrapeTime = alignedScrapeTime
 			}
 		}