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require(raster)

# make 2 dummy rasters, different extents but same origin and resolution. Values 1:6
slope <- raster(xmn = 0, xmx = 5, ymn = 0, ymx = 5, res = 1)
slope[] <- sample(1:6, ncell(slope), replace = T)

soil <- raster(xmn = 0, xmx = 7, ymn = -1, ymx = 4, res = 1)
soil[] <- sample(1:6, ncell(soil), replace = T)

# create your blank raster to populate. This is only the area both inputs occupy.
r_intersec <- raster(intersect(slope,soil))

# The other 2 rasters should be cropped to the extent of your target raster, to avoid extent errors as mentioned in the comments
croped_slope <- crop(slope,extent(r_intersec))
croped_soil <- crop(soil,extent(r_intersec))

tmp <- croped_slope
tmp[which(croped_soil[] <= 0)] <- NA

par(mfrow=c(1,3))
plot(slope)
plot(soil)
plot(tmp)

*raster sample and crop idea from https://gis.stackexchange.com/a/328883/77836

require(raster)

# make 2 dummy rasters, different extents but same origin and resolution. Values 1:6
slope <- raster(xmn = 0, xmx = 5, ymn = 0, ymx = 5, res = 1)
slope[] <- sample(1:6, ncell(slope), replace = T)

soil <- raster(xmn = 0, xmx = 7, ymn = -1, ymx = 4, res = 1)
soil[] <- sample(1:6, ncell(soil), replace = T)

# create your blank raster to populate. This is only the area both inputs occupy.
r_intersec <- raster(raster::intersect(slope,soil))

# The other 2 rasters should be cropped to the extent of your target raster, to avoid extent errors as mentioned in the comments
croped_slope <- crop(slope,extent(r_intersec))
croped_soil <- crop(soil,extent(r_intersec))

tmp <- croped_slope
tmp[which(croped_soil[] <= 0)] <- NA

par(mfrow=c(1,3))
plot(slope)
plot(soil)
plot(tmp)

*raster sample and crop idea from https://gis.stackexchange.com/a/328883/77836

require(raster)

#generate sample rasters
slope <- raster(matrix(c(10,20,30,40,20,30,40,10,30,40,10,20,40,10,20,30),4,4))
plot(slope)

soil <- raster(matrix(c(10,10,10,10,10,20,20,10,0,0,0,0,0,0,0,0),4,4))
plot(soil)

tmp <- slope
tmp[which(soil[] <= 0)] <- NA
plot(tmp)

require(raster)

# make 2 dummy rasters, different extents but same origin and resolution. Values 1:6
slope <- raster(xmn = 0, xmx = 5, ymn = 0, ymx = 5, res = 1)
slope[] <- sample(1:6, ncell(slope), replace = T)
 
soil <- raster(xmn = 0, xmx = 7, ymn = -1, ymx = 4, res = 1)
soil[] <- sample(1:6, ncell(soil), replace = T)

# create your blank raster to populate. This is only the area both inputs occupy.
r_intersec <- raster(intersect(slope,soil))

# The other 2 rasters should be cropped to the extent of your target raster, to avoid extent errors as mentioned in the comments
croped_slope <- crop(slope,extent(r_intersec))
croped_soil <- crop(soil,extent(r_intersec))
 
tmp <- croped_slope
tmp[which(croped_soil[] <= 0)] <- NA 

par(mfrow=c(1,3))
plot(slope)
plot(soil)
plot(tmp)

*raster sample and crop idea from https://gis.stackexchange.com/a/328883/77836

require(raster)

slope <- raster(matrix(c(10,20,30,40,20,30,40,10,30,40,10,20,40,10,20,30),4,4))
soil <- raster(matrix(c(10,10,10,10,10,20,20,10,0,0,0,0,0,0,0,0),4,4))

tmp <- slope
tmp[which(soil[] <= 0)] <- NA
plot(tmp)

require(raster)

#generate sample rasters
slope <- raster(matrix(c(10,20,30,40,20,30,40,10,30,40,10,20,40,10,20,30),4,4))
plot(slope)

soil <- raster(matrix(c(10,10,10,10,10,20,20,10,0,0,0,0,0,0,0,0),4,4))
plot(soil)

tmp <- slope
tmp[which(soil[] <= 0)] <- NA
plot(tmp)