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This is my one line to generate self signed certificates

openssl req -x509 -out localhost.crt -keyout localhost.key \
  -newkey rsa:2048 -nodes -sha256 \
  -subj '/CN=example.com' -extensions EXT -config <( \
   printf "[dn]\nCN=example.com\n[req]\ndistinguished_name = dn\n[EXT]\nsubjectAltName=DNS:example.com\nkeyUsage=digitalSignature\nextendedKeyUsage=serverAuth")

Now I want to sign previous certificates with my own CA so I issue this:

openssl genrsa -des3 -out rootCA.key 4096
openssl req -x509 -new -nodes -key rootCA.key -sha256 -days 1024 -out rootCA.crt

How can I sign with my CA an existing CRT ?

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How can I sign with my CA an existing CRT ?

You can only sign a certificate request but not a certificate. But you can create a certificate request from an existing certificate and then sign this certificate request. See Generate CSR from existing certificate.

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Although this is an unusual thing to do, OpenSSL commandline, which includes a lot of features aimed mainly at debugging problems, can do it. Use openssl x509 (without -req) with -CA certfile -CAkey keyfile or just -CA file if you have both cert and privatekey in one file (which PEM can do). Add -digestname e.g. -sha256 if other than the default (SHA1). You can specify the new serial explicitly with -set_serial, or use almost the same serial-file scheme as openssl ca either by default or explicitly; see man [1ssl?] x509 on your system (unless Windows) or on the web at the heading 'Signing Options' about 1/3 of the way down. (The difference is that ca uses the hex value from the file after incrementing, but x509 [-req] -CA* uses it before. The serial/cert mapping is NOT recorded in a 'database' file, as ca does.) You can specify the length of the validity period, but cannot specify arbitrary start and end times as ca can.

This replaces the issuer name, serial, validity period, and signature, in the new (output) cert, but it does not change any of the extensions, which for your case looks right. If the input cert contains AuthorityKeyIdentifier (AKI) extension to identify its parent/'signing' cert, that extension in the output cert will not correctly identify its parent which may cause trouble in using the cert. You can replace extensions by adding -clrext -extfile filename -extensions section -- but you have to do all of them, which may be inconvenient.

If you use the two-step process of x509 -x509toreq to create a CSR and then either x509 -req -CA* or ca to issue a cert from that CSR, this discards all extensions from the input cert. If you want any extensions you must add them back: for x509 -req -CA* this must be explicit on the command line; for ca it can be configured in the config file or overridden on command line.

ObRant: issuing a cert is often described as 'signing the CSR/request'. It is not. The cert body, aka certTBS (TBS = to-be-signed), is normally based partly on part of the CSR, but most of the cert body is different from the CSR.

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