Magento 2 extremely slow reindexing after server migration (21 hours for 200k products)

After migrating our Magento 2 store to a new dedicated server, we noticed that full reindexing now takes around 21 hours, while on the previous (much weaker) server it used to take about 1 hour.

Server comparison

Old server	New server
4 CPU cores	24 CPU cores
16 GB RAM	128 GB RAM
Reindex time: ~1h	Reindex time: ~21h

We expected indexing time to improve — instead, it got significantly worse.

Store info

Magento 2
~200,000 products
Redis, Elasticsearch, and Varnish are enabled, but I’m not 100% sure if they are configured optimally.
The old server used MariaDB, while the new server uses MySQL 8.0.4.
No major custom changes or new modules after migration

What we’ve done so far

Tuned MySQL config (my.cnf) — see attached
Adjusted settings for both CLI and Apache — see attached php.ini
Confirmed no errors in logs (Magento or MySQL)
MySQL shows high CPU usage during reindexing
Filesystem is SSD-based
php bin/magento indexer:status updates as expected, just extremely slow

What we’re trying to understand

Why reindexing time increased drastically after migration
Whether there are known Magento 2 bottlenecks when moving from server to server
What else could we check (kernel limits, filesystem, MySQL internals, PHP, etc.)

Any tips or direction would be highly appreciated
Please let me know if you’ve encountered similar behavior and what helped in your case.

!includedir /etc/mysql/conf.d/
!includedir /etc/mysql/mysql.conf.d/

[mysqld]
log_bin_trust_function_creators = 1
innodb_buffer_pool_size = 96G
innodb_redo_log_capacity = 512M
innodb_flush_log_at_trx_commit = 2
innodb_flush_method = O_DIRECT
innodb_read_io_threads = 16
innodb_write_io_threads = 16
thread_cache_size = 64
tmp_table_size = 256M
max_heap_table_size = 256M


 PHP CLI Configuration (php.ini for CLI)
 engine = On
short_open_tag = Off
precision = 14
output_buffering = 4096
zlib.output_compression = Off
implicit_flush = Off
serialize_precision = -1
disable_functions =
disable_classes =
zend.enable_gc = On
zend.exception_ignore_args = On
zend.exception_string_param_max_len = 0
expose_php = Off
max_execution_time = 30
max_input_time = 60
memory_limit = 4096M
error_reporting = E_ALL & ~E_DEPRECATED & ~E_STRICT
display_errors = Off
display_startup_errors = Off
log_errors = On
ignore_repeated_errors = Off
ignore_repeated_source = Off
report_memleaks = On
variables_order = "GPCS"
request_order = "GP"
register_argc_argv = Off
auto_globals_jit = On
post_max_size = 8M
auto_prepend_file =
auto_append_file =
default_mimetype = "text/html"
default_charset = "UTF-8"
doc_root =
user_dir =
enable_dl = Off
file_uploads = On
upload_max_filesize = 2M
max_file_uploads = 20
allow_url_fopen = On
allow_url_include = Off
default_socket_timeout = 60
cli_server.color = On
pdo_mysql.default_socket =
SMTP = localhost
smtp_port = 25
mail.add_x_header = Off
mail.mixed_lf_and_crlf = Off
odbc.allow_persistent = On
odbc.check_persistent = On
odbc.max_persistent = -1
odbc.max_links = -1
odbc.defaultlrl = 4096
odbc.defaultbinmode = 1
mysqli.max_persistent = -1
mysqli.allow_persistent = On
mysqli.max_links = -1
mysqli.default_port = 3306
mysqli.default_socket =
mysqli.default_host =
mysqli.default_user =
mysqli.default_pw =
mysqlnd.collect_statistics = On
mysqlnd.collect_memory_statistics = Off
pgsql.allow_persistent = On
pgsql.auto_reset_persistent = Off
pgsql.max_persistent = -1
pgsql.max_links = -1
pgsql.ignore_notice = 0
pgsql.log_notice = 0
bcmath.scale = 0
session.save_handler = files
session.use_strict_mode = 0
session.use_cookies = 1
session.use_only_cookies = 1
session.name = PHPSESSID
session.auto_start = 0
session.cookie_lifetime = 0
session.cookie_path = /
session.serialize_handler = php
session.gc_probability = 0
session.gc_divisor = 1000
session.gc_maxlifetime = 1440
session.cache_limiter = nocache
session.cache_expire = 180
session.use_trans_sid = 0
session.sid_length = 26
session.trans_sid_tags = "a=href,area=href,frame=src,form="
session.sid_bits_per_character = 5
soap.wsdl_cache_enabled = 1
soap.wsdl_cache_dir = "/tmp"
soap.wsdl_cache_ttl = 86400
soap.wsdl_cache_limit = 5
ldap.max_links = -1
tidy.clean_output = Off
zend.assertions = -1




PHP Apache2 Configuration (php.ini for Apache)

engine = On
short_open_tag = Off
precision = 14
output_buffering = 4096
zlib.output_compression = Off
implicit_flush = Off
serialize_precision = -1
disable_functions =
disable_classes =
zend.enable_gc = On
zend.exception_ignore_args = On
zend.exception_string_param_max_len = 0
expose_php = Off
max_execution_time = 30
max_input_time = 60
memory_limit = 4096M
error_reporting = E_ALL & ~E_DEPRECATED & ~E_STRICT
display_errors = Off
display_startup_errors = Off
log_errors = On
ignore_repeated_errors = Off
ignore_repeated_source = Off
report_memleaks = On
variables_order = "GPCS"
request_order = "GP"
register_argc_argv = Off
auto_globals_jit = On
post_max_size = 8M
default_mimetype = "text/html"
default_charset = "UTF-8"
doc_root =
user_dir =
enable_dl = Off
file_uploads = On
upload_max_filesize = 2M
max_file_uploads = 20
allow_url_fopen = On
allow_url_include = Off
default_socket_timeout = 60
cli_server.color = On
pdo_mysql.default_socket =
SMTP = localhost
smtp_port = 25
mail.add_x_header = Off
mail.mixed_lf_and_crlf = Off
odbc.allow_persistent = On
odbc.check_persistent = On
odbc.max_persistent = -1
odbc.max_links = -1
odbc.defaultlrl = 4096
odbc.defaultbinmode = 1
mysqli.max_persistent = -1
mysqli.allow_persistent = On
mysqli.max_links = -1
mysqli.default_port = 3306
mysqli.default_socket =
mysqli.default_host =
mysqli.default_user =
mysqli.default_pw =
mysqlnd.collect_statistics = On
mysqlnd.collect_memory_statistics = Off
pgsql.allow_persistent = On
pgsql.auto_reset_persistent = Off
pgsql.max_persistent = -1
pgsql.max_links = -1
pgsql.ignore_notice = 0
pgsql.log_notice = 0
bcmath.scale = 0
session.save_handler = files
session.use_strict_mode = 0
session.use_cookies = 1
session.use_only_cookies = 1
session.name = PHPSESSID
session.auto_start = 0
session.cookie_lifetime = 0
session.cookie_path = /
session.serialize_handler = php
session.gc_probability = 0
session.gc_divisor = 1000
session.gc_maxlifetime = 1440
session.cache_limiter = nocache
session.cache_expire = 180
session.use_trans_sid = 0
session.sid_length = 26
session.trans_sid_tags = "a=href,area=href,frame=src,form="
session.sid_bits_per_character = 5
soap.wsdl_cache_enabled = 1
soap.wsdl_cache_dir = "/tmp"
soap.wsdl_cache_ttl = 86400
soap.wsdl_cache_limit = 5
ldap.max_links = -1
tidy.clean_output = Off
zend.assertions = -1