You can reorder the levels of the Condition column using the factor() function.
library(ggplot2)
DF <- data.frame(Sample = rep(c("A", "B", "C"), each = 3),
Percent = c(20,20, 60, 25, 35, 40, 30, 20, 50),
Condition = c("JAR", "strong", "weak", "JAR", "strong", "weak",
"JAR", "strong", "weak"))
DF
#> Sample Percent Condition
#> 1 A 20 JAR
#> 2 A 20 strong
#> 3 A 60 weak
#> 4 B 25 JAR
#> 5 B 35 strong
#> 6 B 40 weak
#> 7 C 30 JAR
#> 8 C 20 strong
#> 9 C 50 weak
ggplot() + geom_bar(aes(y = Sample, x = Percent, fill = Condition), data = DF,
stat="identity") +
scale_fill_manual(values = c("#669999", "#CCCCCC","#FFFFFF")) +
theme(axis.title.x=element_blank())

#Reorder the levels of Condition
DF$Condition = factor(DF$Condition, levels = c("weak", "JAR", "strong"))
ggplot() + geom_bar(aes(y = Sample, x = Percent, fill = Condition), data = DF,
stat="identity") +
scale_fill_manual(values = c("#669999", "#CCCCCC","#FFFFFF")) +
theme(axis.title.x=element_blank())

Created on 2020-06-21 by the reprex package (v0.3.0)