MariaDB 5.3 and beyond have a number of features that are targeted at big queries and so are disabled by default.

This page describes recommended settings for IO-bound queries that shovel through lots of records.

First, turn on Batched Key Access:

# Turn on disk-ordered reads
optimizer_switch='mrr=on'
optimizer_switch='mrr_cost_based=off'

# Turn on Batched Key Access (BKA)
join_cache_level = 6

Give BKA buffer space to operate on. Ideally, it should have enough space to fit all the data examined by the query.

# Size limit for the whole join
join_buffer_space_limit = 300M

# Limit for each individual table
join_buffer_size = 100M

Turn on index_merge/sort-intersection:

optimizer_switch='index_merge_sort_intersection=on'

If your queries examine big fraction of the tables (somewhere more than ~ 30%), turn on hash join:

# Turn on both Hash Join and Batched Key Access
join_cache_level = 8